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revision 1431, Wed Aug 23 22:13:53 2006 UTC revision 2050, Tue Aug 14 22:23:33 2007 UTC
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1  2006-08-23  Douglas Bates  <bates@dyn-51-128.uwnet.wisc.edu>  2007-08-14 13:07  Douglas Bates <bates@stat.wisc.edu>
2    
3          * R/AllClass.R,src/SOURCES_C.mkf,init.c,NAMESPACE: Remove classes          * [r4730] src/Mutils.h: declare alloca
4          lCholCMatrix and dCholCMatrix based on R_ldl code.          * [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    
12    2007-08-14  Martin Maechler  <maechler@stat.math.ethz.ch>
13    
14            * R/nearPD.R, man/nearPD.Rd (nearPD): new function built on Jens
15            Oehlschlaegel's ... result type still to be discussed!
16    
17    2007-08-10  Martin Maechler  <maechler@stat.math.ethz.ch>
18    
19            * man/image-methods.Rd: new, combining all image() methods
20    
21    2007-08-09  Martin Maechler  <maechler@stat.math.ethz.ch>
22    
23            * R/dgCMatrix.R: define qr() and lu() methods for "sparseMatrix"
24            to work via dgC...
25    
26            * R/Matrix.R (Matrix): special treatment for "table" (S3)
27    
28    2007-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
29    
30            * R/dgTMatrix.R (image): change defaults to
31                    aspect = "iso", colorkey = FALSE
32    
33    2007-08-06  Martin Maechler  <maechler@stat.math.ethz.ch>
34    
35            * src/dsyMatrix.c (dsyMatrix_matrix_mm): 'b' might be matrix;
36            must copy its *expanded* x slot before LAPACK call.
37    
38            * tests/matprod.R: test the last days' changes.
39    
40    2007-08-06 16:43  Douglas Bates <bates@stat.wisc.edu>
41    
42            * [r4712] inst/include/Matrix_stubs.c: Change R_cholmod_printf in stubs
43              as well as in sources
44            * [r4713] src/dsyMatrix.c: Duplicate the contents of the RHS before
45              Lapack call
46    
47    2007-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
48    
49            * R/Matrix.R (%*%, crossprod, tcrossprod): add method for
50                    ("Matrix", "matrix") which is needed in some cases.
51            Ditto for solve().
52    
53            * R/colSums.R (.as.dge.Fun): need ddenseMatrix methods to avoid
54            infinite recursion in dispatch for some cases.
55    
56    2007-08-02 08:48  Martin Maechler <maechler@stat.math.ethz.ch>
57    
58            * [r4693] src/chm_common.c: R_cholmod_printf() instead of Rprintf() just
59              so pointers match
60    
61    2007-08-02  Martin Maechler  <maechler@stat.math.ethz.ch>
62    
63            * DESCRIPTION (Date): set ready for release -- 0.999375-1
64    
65    2007-08-01 15:44  Douglas Bates <bates@stat.wisc.edu>
66    
67            * [r4686] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
68              src/chm_common.c, src/chm_common.h: Change API for
69              numeric_as_chm_dense and N_AS_CHM_DN
70    
71    2007-08-01  Martin Maechler  <maechler@stat.math.ethz.ch>
72    
73            * src/dtrMatrix.c (dtrMatrix_matrix_mm): fix dimensionality check (!)
74            * tests/matprod.R: regr.test for it
75    
76    2007-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
77    
78            * R/dMatrix.R: fix from Brian for   Math2(., digits = "missing")
79            * tests/group-methods.R: and regression-test it
80    
81    2007-07-19 19:45  Douglas Bates <bates@stat.wisc.edu>
82    
83            * [r4642] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
84              inst/include/cholmod.h, src/chm_common.c, src/init.c: Export
85              triplet_to_sparse, documentation, use typedefs
86    
87    2007-07-18  Martin Maechler  <maechler@stat.math.ethz.ch>
88    
89            * man/dpoMatrix-class.Rd: added 'corMatrix' example
90    
91            * src/dsyMatrix.[ch] (dsyMatrix_as_matrix): new 'keep_dimnames' arg
92            * src/dtrMatrix.[ch] (dtrMatrix_as_matrix): ditto
93            * src/init.c, R/dsyMatrix.R, R/dtrMatrix.R, R/lgTMatrix.R: ditto
94    
95            * R/lsparseMatrix.R: bug fix in "all" method
96            * R/Ops.R (.do.Logic.lsparse): "|" bug in borderline case
97    
98            * R/dsyMatrix.R (coerce->dsTMatrix): (i,j) slots should *not* have names
99            * R/ngTMatrix.R (coerce->ngTMatrix): ditto;
100                    + matrix |-> nMatrix coercion
101            * R/pMatrix.R: + setAs()  to dMatrix and from nMatrix
102            * man/pMatrix-class.Rd: ditto
103    
104            * R/Matrix.R (Summary): method for non-dMatrix
105    
106            * tests/Class+Meth.R (extraValid): new check about "dirty" slots
107            * tests/Class+Meth.R (tstMatrixClass): test norm(.);
108                    test all Summary methods.
109    
110    2007-07-16  Martin Maechler  <maechler@stat.math.ethz.ch>
111    
112            * R/dgeMatrix.R (norm, rcond): methods for 'matrix'
113    
114    2007-07-14  Martin Maechler  <maechler@stat.math.ethz.ch>
115    
116            * R/sparseMatrix.R (norm): simple methods for sparseMatrix
117    
118            * R/pMatrix.R (t?crossprod): methods for pMatrix
119    
120    2007-07-10  Douglas Bates  <bates@stat.wisc.edu>
121    
122            * src/dgeMatrix.c (dgeMatrix_colsums): Get the logic straight.
123    
124    2007-07-09 20:45  Douglas Bates <bates@stat.wisc.edu>
125    
126            * [r4579] src/dgeMatrix.c: Untangle horrible code in dgeMatrix_colsums
127              trying to fix a subtle bug - which has been somewhere else.
128    
129    2007-07-09 19:43  Martin Maechler <maechler@stat.math.ethz.ch>
130    
131            * [r4578] src/dgeMatrix.c: "cleaned" dgeMatrix_colsums() - but did not
132              solve the bug
133    
134    2007-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
135    
136            * src/dgCMatrix.c (compressed_to_TMatrix):
137    
138    2007-07-07  Martin Maechler  <maechler@stat.math.ethz.ch>
139    
140            * src/Csparse.c (Rsparse_validate): new, to have some validity
141            checking for RsparseMatrix
142            * src/dgCMatrix.c (xRMatrix_validate): ditto
143            * src/dtCMatrix.c (tRMatrix_validate): ditto
144    
145    2007-07-07  Douglas Bates <bates@stat.wisc.edu>
146    
147            * [r4567] R/AllClass.R: Slots already in RsparseMatrix were redefined in
148              lgRMatrix
149            * [r4568] DESCRIPTION: Prepare for bug-fix release
150            * [r4570] src/CHOLMOD/Check/cholmod_write.c: Include cholmod_matrixops.h
151              for declaration of cholmod_symmetry
152    
153    2007-07-06  Martin Maechler  <maechler@stat.math.ethz.ch>
154    
155            * DESCRIPTION (Version): 0.999375 merged into the trunk; ready for
156            release.
157    
158    2007-07-06 14:11  Douglas Bates <bates@stat.wisc.edu>
159    
160            * [r4559] src/iohb.c, src/iohb.h: Remove Harwell-Boeing input/output
161              functions - no longer used
162            * [r4560] src/HBMM.c, src/Mutils.c, src/dgTMatrix.c, src/dgeMatrix.c,
163              src/dspMatrix.c, src/dsyMatrix.c, src/dtCMatrix.c,
164              src/factorizations.c, src/sparseQR.c: Replace most calls to Calloc by
165              Alloca
166    
167    2007-07-06 13:14  Martin Maechler <maechler@stat.math.ethz.ch>
168    
169            * [r4558] inst/doc/Comparisons.Rnw, src/CHMfactor.c, src/Csparse.c,
170              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dense.c,
171              src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c, src/sparseQR.c,
172              src/t_gCMatrix_colSums.c: more R_CheckStack()s
173    
174    2007-07-05 18:12  Douglas Bates <bates@stat.wisc.edu>
175    
176            * [r4550] inst/include/Matrix.h: Add the macro N_AS_CHM_DN to "alloca"
177              the required amount of memory then call M_numeric_as_chm_dense.
178            * [r4556] src/Mutils.h, src/dgCMatrix.c: Define and use the Alloca macro
179              (like Calloc but calling alloca)
180    
181    2007-07-05  Martin Maechler  <maechler@stat.math.ethz.ch>
182    
183            * R/sparseMatrix.R (printSpMatrix): renamed from prSpMatrix()
184            and extended with more sophisticated 'col.names' option.
185            * NAMESPACE: export  printSparseMatrix()
186            * man/printSpMatrix.Rd: document, incl. examples
187    
188    2007-07-04 16:21  Douglas Bates <bates@stat.wisc.edu>
189    
190            * [r4543] src/cs_utils.c, src/cs_utils.h, src/dgCMatrix.c,
191              src/dtCMatrix.c, src/sparseQR.c: CSP typedef for *cs and macro
192              AS_CSP. API change - pass the empty structure to Matrix_as_cs.
193    
194    2007-07-04  Martin Maechler  <maechler@stat.math.ethz.ch>
195    
196            * DESCRIPTION (Version): 0.99875-4
197    
198            * tests/Class+Meth.R (tstMatrixClass): add dimnames, and hence test
199            some dimnames perservation.
200    
201            * R/dsTMatrix.R (t-method): keep dimnames
202            * R/dtTMatrix.R:  ditto
203    
204            * R/sparseMatrix.R (prSpMatrix): print colnames when non-trivial
205            and ncol(.) < 10
206    
207            * src/cs_utils.c: drop check_class() and use Matrix_check_class()
208            from Mutils.h
209    
210            * src/lgCMatrix.c ([ln]csc_to_matrix): no longer lose dimnames,
211            e.g. in as(<ngCMatrix>, "matrix")
212    
213    2007-07-01 13:27  Douglas Bates <bates@stat.wisc.edu>
214    
215            * [r4529] .: Create a branch for the API changes from the 0.99875
216              series to the 0.999375 series
217            * [r4530] DESCRIPTION, inst/include/Matrix.h,
218              inst/include/Matrix_stubs.c, src/CHMfactor.c, src/Csparse.c,
219              src/Mutils.h, src/Tsparse.c, src/chm_common.c, src/chm_common.h,
220              src/dense.c, src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c,
221              src/t_gCMatrix_colSums.c: API change - pass the empty structure to the
222              as_cholmod_x functions
223    
224    2007-06-30 09:05  Martin Maechler <maechler@stat.math.ethz.ch>
225    
226            * [r4527] trunk/Matrix/DESCRIPTION, trunk/Matrix/NAMESPACE,
227              trunk/Matrix/inst/doc/Comparisons.Rnw: add session- and hardware-info
228              to Comparisons
229    
230    >>>>>>> .merge-right.r4561
231    2007-06-29  Martin Maechler  <maechler@stat.math.ethz.ch>
232    
233            * DESCRIPTION (Version): 0.99875-3 ready to be released.
234    
235            * R/sparseMatrix.R (spMatrix): make spMatrix(3,4) working
236    
237            * R/AllGeneric.R: set "Math" (and "Math2") group generics in a way
238            that should also work in a future version of R.
239    
240    2007-06-21  Martin Maechler  <maechler@stat.math.ethz.ch>
241    
242            * NAMESPACE, R/AllClass.R: "xsparseVector" class union.
243    
244            * R/sparseVector.R: more *sparseVector coercions, notably for
245            non - double ones.
246    
247    2007-06-19  Martin Maechler  <maechler@stat.math.ethz.ch>
248    
249            * R/colSums.R: new file for all (col|row)(Sums|Means) methods,
250              notably the new ones building on the new .Call(.)s:
251    
252            * src/dgCMatrix.c (DEF_gCMatrix_COLSUMS): use to define
253            all 4 of [dlin]gCMatrix_colSums().
254    
255    2007-06-18 16:12  Douglas Bates <bates@stat.wisc.edu>
256    
257            * [r4472] src/Syms.h, src/init.c: Added Matrix_lengthSym
258            * [r4473] src/dgCMatrix.c: Modified dgCMatrix_colSums for sparseVector
259              result
260    
261    2007-06-16  Martin Maechler  <maechler@stat.math.ethz.ch>
262    
263            * R/kronecker.R: fix typo (could lead to inf.recursion)
264            * test/simple.R: testing that
265    
266            * R/sparseMatrix.R (prSpMatrix): change to be used as print()
267            method as well (which can have arguments, show() can't).
268    
269    2007-06-16 15:52  Douglas Bates <bates@stat.wisc.edu>
270    
271            * [r4466] R/dgCMatrix.R, src/dgCMatrix.c, src/dgCMatrix.h, src/init.c:
272              added dgCMatrix_colSums for [col,row][Sums,Means]
273    
274    2007-06-15 23:15  Douglas Bates <bates@stat.wisc.edu>
275    
276            * [r4460] R/sparseMatrix.R, man/dgCMatrix-class.Rd, src/dgCMatrix.c,
277              src/dgCMatrix.h, src/init.c: added lm.fit.sparse (unexported),
278              coercion of "factor" to "dgCMatrix" and dgCMatrix_cholsol
279            * [r4461] R/AllClass.R, man/sparseMatrix-class.Rd: draft "indicators"
280              class
281            * [r4463] R/sparseMatrix.R, man/dgCMatrix-class.Rd,
282              man/sparseMatrix-class.Rd: Don't need an "indicators" class - use the
283              row names to store the levels - duh!  Added an example.
284    
285    2007-06-14  Martin Maechler  <maechler@stat.math.ethz.ch>
286    
287            * src/Csparse.c (Csparse_validate): check for *repeated* entries
288            thanks to example from Christian Buchta; with a test here:
289            * tests/simple.R:
290    
291    2007-06-07  Martin Maechler  <maechler@stat.math.ethz.ch>
292    
293            * R/Auxiliaries.R (callGeneric): another fix, needed for some cases
294            of colSums(*, sparseResult = TRUE)
295    
296    2007-06-06  Martin Maechler  <maechler@stat.math.ethz.ch>
297    
298            * R/lsparseMatrix.R, R/ldenseMatrix.R (all, any): change default to
299            'na.rm = FALSE' as "everywhere" else in R.
300    
301    2007-06-05 Douglas Bates <bates@stat.wisc.edu>
302    
303            * [r4421] src/CSparse_install.sh: Modify for new organization of
304              CSparse package
305            * [r4425] src/UFsparse_download.sh: Update to version 3.0.0 of
306              SuiteSparse
307            * [r4426] src/Makefile: add ./UFconfig to the include path for
308              compilation
309            * [r4427] src/cs.[ch]: update to CSparse version 2.2.0
310            * [r4428] inst/doc/UFsparse/* src/{AMD,CHOLMOD,COLAMD}/*
311              src/UFconfig/UFconfig.h: Update to version 3.0.0 of SuiteSparse
312    
313    2007-06-05  Martin Maechler  <maechler@stat.math.ethz.ch>
314    
315            * R/Auxiliaries.R (emptyColnames): + argument msg.if.not.empty, used in
316            * R/sparseMatrix.R (prSpMatrix): now gives a message about
317            suppressed column names.
318    
319    2007-06-04 17:13  Douglas Bates <bates@stat.wisc.edu>
320    
321            * [r4418] src/Csparse.c, src/HBMM.c, src/Mutils.c, src/Mutils.h,
322              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dgCMatrix.c,
323              src/dgeMatrix.c, src/dpoMatrix.c, src/dpoMatrix.h, src/dppMatrix.c,
324              src/dppMatrix.h, src/dsCMatrix.c, src/dspMatrix.c, src/dspMatrix.h,
325              src/dsyMatrix.c, src/dsyMatrix.h, src/dtpMatrix.c, src/dtrMatrix.c:
326              Remove warnings after change to const char* CHAR
327    
328    2007-06-04 17:11  Douglas Bates <bates@stat.wisc.edu>
329    
330            * [r4417] inst/include/Matrix_stubs.c, inst/include/cholmod.h: Corrected
331              type of M_cholmod_ssmult
332    
333    2007-06-03 14:42  Douglas Bates <bates@stat.wisc.edu>
334    
335            * [r4412] inst/include/Matrix_stubs.c, inst/include/cholmod.h,
336              src/init.c: Yet another cholmod export - cholmod_ssmult
337    
338    2007-05-23  Martin Maechler  <maechler@stat.math.ethz.ch>
339    
340            * NAMESPACE: exported drop0(), since
341            * man/drop0.Rd: I have seen several cases, I really wanted to use
342            it, so our users may want too.
343    
344    2007-05-22  Martin Maechler  <maechler@stat.math.ethz.ch>
345    
346            * man/colSums.Rd: separately document colSums() etc, since these
347            have the extra argument 'sparseResult'.
348    
349    2007-05-21  Martin Maechler  <maechler@stat.math.ethz.ch>
350    
351            * R/sparseMatrix.R (spMatrix): utility (T)sparse Matrix constructor;
352            * man/spMatrix.Rd: docu., including examples
353    
354            * R/Auxiliaries.R (sp.colMeans): etc, using a patched callGeneric(),
355            in order to make colMeans() etc fast *and* correct.
356            * R/sparseVector.R (replSPvec): "[<-" functionality for
357            sparseVectors; tested in
358            * tests/simple.R:
359    
360    2007-05-19  Martin Maechler  <maechler@stat.math.ethz.ch>
361    
362            * R/sparseMatrix.R (print.sparseSummary): and summary() method for
363            (very) sparse Matrices; output similar to Matlab's print().
364    
365    2007-05-17  Douglas Bates  <bates@stat.wisc.edu>
366    
367            * src/HBMM.c (Matrix_writeMatrixMarket): Write 1-based, not
368            0-based, indices (Jose Quesada <quesada@gmail.com>).
369    
370    2007-05-16  Douglas Bates  <bates@stat.wisc.edu>
371    
372            * R/CHMfactor.R: Added solve methods for a CHMfactor object.
373    
374    2007-05-16  Martin Maechler  <maechler@stat.math.ethz.ch>
375    
376            * R/Auxiliaries.R (sparsapply): new utility, much faster than
377            tapply1() for large sparse matrices.
378    
379    2007-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
380    
381            * R/Matrix.R (dim<-): reshape now via sparseVector.
382    
383            * R/sparseVector.R: methods and function for
384            * R/AllClass.R: new "sparseVector" class and daughters.
385            * NAMESPACE: export new classes
386    
387    2007-05-14  Martin Maechler  <maechler@stat.math.ethz.ch>
388    
389            * DESCRIPTION (Version): 0.99875-1
390            * src/Makefile.win: also remove Lapack code from here (cf. 04-25).
391    
392    2007-05-11  Martin Maechler  <maechler@stat.math.ethz.ch>
393    
394            * R/Tsparse.R ([, Tsparse): fix last case: *duplicated*, symmetric
395            indexing
396            * tests/indexing.R: test set for that.
397    
398    2007-05-08  Martin Maechler  <maechler@stat.math.ethz.ch>
399    
400            * R/Tsparse.R (replTmat): fix the case of *duplicated* index
401            entries.
402            * tests/indexing.R(out): add regression test for it
403    
404    2007-04-30  Martin Maechler  <maechler@stat.math.ethz.ch>
405    
406            * R/(l(dense|sparse))?Matrix.R (!): use 'x', not 'e1' as argument
407            name for "!" method definitions.
408    
409    2007-04-26  Martin Maechler  <maechler@stat.math.ethz.ch>
410    
411            * R/Tsparse.R (intI): new utility, used for "[" :
412                    Cleanup up there, and fixes for duplicated indices - more TODO!
413    
414            * tests/indexing.R(out): more tests
415    
416    2007-04-25  Douglas Bates  <bates@stat.wisc.edu>
417    
418            * DESCRIPTION,src/Makefile: require R>= 2.5.0 and remove Lapack
419            code that is now part of the R Lapack library.
420    
421            * src/init.c,inst/include/{Matrix_stubs.c,cholmod.h}:export
422            cholmod_factorize_p (used in lme4 for GLMMs and NLMMs).
423    
424    2007-04-21  Martin Maechler  <maechler@stat.math.ethz.ch>
425    
426            * R/Matrix.R (image): method for all Matrices, not just sparse ones.
427    
428    2007-04-17  Martin Maechler  <maechler@stat.math.ethz.ch>
429    
430            * R/Auxiliaries.R (tapply1): unname(.) -> colSums() etc don't end
431            up with extraneous names '0'...'<n-1>'
432    
433    2007-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
434    
435            * R/dgTMatrix.R (mat2dgT): care about NAs
436    
437    2007-04-11  Martin Maechler  <maechler@stat.math.ethz.ch>
438    
439            * R/kronecker.R: triangularity preserving methods
440    
441    2007-03-27  Martin Maechler  <maechler@stat.math.ethz.ch>
442    
443            * R/kronecker.R: new file collecting kronecker() methods in one
444                    place.  Goal: become much faster!
445    
446    2007-03-23  Martin Maechler  <maechler@stat.math.ethz.ch>
447    
448            * src/dtCMatrix.c (dtCMatrix_solve): use the new code from Kasper
449            Kristensen based cs_spsolve() instead of _lsolve & _usolve which
450            can be much faster.
451    
452            * tests/matprod.R: add regression tests for these (upper & lower).
453    
454    2007-03-19  Martin Maechler  <maechler@stat.math.ethz.ch>
455    
456            * R/Matrix.R (diff): method for our Matrices.
457    
458            * R/sparseMatrix.R (isDiagonal): check dim()!
459    
460    2007-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
461    
462            * R/Matrix.R (dim<-): new method for "reshape()" built on a
463            proposal from Tamas Papp.
464    
465    2007-03-16  Martin Maechler  <maechler@stat.math.ethz.ch>
466    
467            * R/AllGeneric.R: remove all  if(!isGeneric(.))  clauses
468    
469            * R/zzz.R (.onLoad, .onUnload): do *not* leave bind_activation(TRUE);
470            rather define and export  cBind() and rBind() only.
471            --> useRs *must* change code that used to have cbind()/rbind() !!
472    
473            * R/bind.R: change tests from cbind() to cBind() and similarly to rBind()
474            * R/bind.Rout.save: ditto
475    
476    2007-02-16  Douglas Bates  <bates@r-project.org>
477    
478            * DESCRIPTION (Date, Version): 0.9975-11 with new date
479            * src/dgCMatrix.c (R_to_CMatrix, compressed_to_TMatrix): remove
480            const modifier on declaration of the array 'valid'
481    
482    2007-02-12  Douglas Bates  <bates@stat.wisc.edu>
483    
484            * R/CHMfactor.R: Add image method (coercion to sparseMatrix).
485    
486    2007-02-05  Martin Maechler  <maechler@stat.math.ethz.ch>
487    
488            * DESCRIPTION (Date, Version): 0.9975-10 with new date.
489    
490            * R/Ops.R (Arith): make sure Csparse o Csparse also works for e.g. ntCMatrix
491            * tests/simple.R: test the above and some of these coercions:
492    
493            * R/nsparseMatrix.R: coercing "Csparse" to "lsparseMatrix";
494                    be careful to avoid infinite recursion, using new coercions in
495            * R/ngCMatrix.R and nsC... and ntC...
496            * R/lsparseMatrix.R: ditto
497    
498            * R/SparseM-conv.R: more conversion, notably for triplet matrices.
499    
500            * src/dgCMatrix.c (R_to_C_Matrix): port Doug's fix and
501            * R/Rsparse.R: reactivate .Call()s
502    
503            * tests/Class+Meth.R: a bit more on actual classes
504    
505    2007-02-04  Douglas Bates  <bates@stat.wisc.edu>
506    
507            * src/dgCMatrix.c (compressed_to_TMatrix): fix memory bug using strdup()
508    
509    2007-02-03  Martin Maechler  <maechler@stat.math.ethz.ch>
510    
511            * DESCRIPTION (Version): 0.9975-10 to upload
512    
513            * tests/Class+Meth.R (tstMatrixClass): require coercions to
514            specific classes less unconditionally.
515    
516            * R/Auxiliaries.R: get rid of as_Tsparse() and as_Rsparse()
517    
518            * R/Tsparse.R (triu): etc, use as(*, "TsparseMatrix") instead of as_Tsparse()
519    
520            * R/Rsparse.R (.R.2.T): R-level workaround using compressed_to_TMatrix.
521            * R/Rsparse.R (.R.2.C): R-level workaround since C-level
522            R_to_CMatrix segfaults on one platform.
523            Eliminate most coercion method to *specific* classes, and replace
524            with virtual classes coercions.
525    
526    
527    2007-02-01  Martin Maechler <maechler@stat.math.ethz.ch>
528    
529            * src/init.c: export the CHM...._validate() placeholders, since
530            they *are* called.
531    
532            * tests/Class+Meth.R (classCanCoerce): and starting to test
533            all as(<from>, <to>)
534    
535    2007-01-30  Martin Maechler  <maechler@stat.math.ethz.ch>
536    
537            * R/Tsparse.R ([): more care when subsetting triangular Tsparse
538            * tests/indexing.R: tested now
539            * tests/indexing.Rout.save: updated
540    
541            * src/Csparse.c (Csparse_to_dense): use Rkind = -1 for PATTERN to
542            * src/chm_common.c (chm_dense_to_SEXP): return "ngeMatrix" when
543            appropriate.
544    
545            * NAMESPACE: export a trivial
546            * R/Matrix.R: drop() Matrix-method
547    
548            * R/AllClass.R: moved all prototypes to virtual super classes.
549    
550            * R/Rsparse.R: many more coercions to have less exceptions in
551            * tests/Class+Meth.R:
552    
553            * R/Ops.R (Compare): tweak for case with NA
554            * tests/simpl.R: hence another 'FIXME' eliminated
555    
556    2007-01-29  Martin Maechler  <maechler@stat.math.ethz.ch>
557    
558            * R/diagMatrix.R (solve): the obvious methods for diagonalMatrix
559            objects.
560    
561            * tests/Class+Meth.R (tstMatrixClass): now testing diag(), nnzero(),
562              and more of "!", "&", "|", all, any; coercions
563    
564            * R/Rsparse.R: many coercions (which enable quite a few other
565            methods), thanks to enhancements in
566            * src/dgCMatrix.c (R_to_CMatrix): new, and
567            * src/dgCMatrix.c (compressed_to_TMatrix): now for (d,l,n) ,
568            symmetric & triangular and ..RMatrix objects.
569    
570            * src/TMatrix_as.c (Matrix_T_as_DENSE,Matrix_T_as_GENERAL):
571            renamed file from src/dsTMatrix.c;
572            now dealing with symmetric and triangular Tsparse coercions, both
573            to dense and general.
574    
575    2007-01-27  Martin Maechler  <maechler@stat.math.ethz.ch>
576    
577            * src/dsTMatrix.c: has now "l" and "n" methods besides the "d" ones.
578    
579            * R/Ops.R (Arith): <dgCMatrix> o <numeric> now remains sparse
580            where sensible when the <numeric> is of length > 1.
581    
582    2007-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
583    
584            * R/Matrix.R ([<-): for M[] <- value: fix length
585    
586    2007-01-25  Martin Maechler  <maechler@stat.math.ethz.ch>
587    
588            * R/Auxiliaries.R (n2l_Matrix): new, to be used in
589            * R/ndenseMatrix.R: new coercions n* -> l*
590    
591    2007-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
592    
593            * R/triangularMatrix.R: new file; simple triu() and tril() methods.
594    
595            * R/Ops.R ("Logic"): and other "Ops", many updates
596    
597    2007-01-18  Martin Maechler  <maechler@stat.math.ethz.ch>
598    
599            * src/Mutils.h (SET_DimNames): new utility
600    
601            * R/Auxiliaries.R (nnzero): improved and now exported via
602    
603            * NAMESPACE: + nnzero(); length() == prod(dim(.)) method for all "Matrix" objects
604    
605    2007-01-17  Martin Maechler  <maechler@stat.math.ethz.ch>
606    
607            * R/diagMatrix.R (!): fix typo.
608    
609    2007-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
610    
611            * R/Auxiliaries.R (as_Csparse): and quite a few others:
612                    allow to pass class definition --> speedup
613            * R/sparseMatrix.R: apply the above
614    
615            * R/Csparse.R: coercion Csparse* to dense* now preserves shape properties.
616    
617            * src/Mutils.h (mMatrix_as_geMatrix): new, based on
618            * src/Mutils.c (dup_mMatrix_as_geMatrix): new; generalization of
619            old dup_mMatrix_as_dgeMatrix), eliminating a long-standing "FIXME".
620    
621            * src/dense.c (dense_to_Csparse): use new mMatrix_as_geMatrix()
622    
623            * R/denseMatrix.R (.dense2C): based on dense_to_Csparse: name it,
624            and use it for "sparse*" as well, since it's faster than the
625            as_Csparse(.) way.
626    
627    2007-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
628    
629            * R/Ops.R ("Logic"): more methods, notably an  <lgC> o <lgC> one.
630    
631    2007-01-12  Martin Maechler  <maechler@stat.math.ethz.ch>
632    
633            * R/Tsparse.R (.TM.repl.i.2col): new internal function to be used
634            as method for   M[ ij ] <- v
635            * R/Csparse.R:: go via Tsparse for "M[ij] <- v"
636    
637            * R/Ops.R: "Compare" for (C|R)sparse: need pointer slot for all
638            FALSE answer
639    
640            * R/Csparse.R (replCmat): fix the "all non-zero" case with reordering
641            * tests/indexing.R: test it, and some of the above
642    
643    2007-01-05  Martin Maechler  <maechler@stat.math.ethz.ch>
644    
645            * R/Auxiliaries.R (is_duplicatedT): new utility
646    
647    2007-01-05  Douglas Bates  <bates@stat.wisc.edu>
648    
649            * src/init.c (R_init_Matrix): export cholmod_scale
650    
651    2006-12-30  Martin Maechler  <maechler@stat.math.ethz.ch>
652    
653            * R/zzz.R (tmp): for R >= 2.5.0, extend formals of our
654            base::as.matrix to (x, ...)
655    
656    2006-12-28  Martin Maechler  <maechler@stat.math.ethz.ch>
657    
658            * R/Ops.R ("Arith" etc): move almost all "Ops" methods to new R
659            file; start using "Logic", hence
660    
661            * DESCRIPTION (Depends): R >= 2.4.1 (since we want "Logic")
662            * NAMESPACE: import and export "Logic"
663    
664    2006-12-27  Martin Maechler  <maechler@stat.math.ethz.ch>
665    
666            * src/zpotfr.f and dependencies: use LAPACK 3.1 version
667            only needed previously to R version 2.5.0.
668    
669    2006-12-26  Martin Maechler  <maechler@stat.math.ethz.ch>
670    
671            * DESCRIPTION (Date, Version): 0.9975-8, ready for release
672    
673            * R/Tsparse.R (replTmat): fix subassignment of triangular
674            * R/Csparse.R (replCmat): ditto
675            * tests/indexing.R: more tests, incl the above fix
676    
677    2006-12-23  Martin Maechler  <maechler@stat.math.ethz.ch>
678    
679            * R/Auxiliaries.R (drop0): extend for non CSparse
680            * R/Auxiliaries.R (diagU2N): should work for all sparseMatrix
681    
682            * src/Csparse.c (Csparse_to_Tsparse, Csparse_general_to_symmetric):
683                    use uplo correctly (!); other places: use uplo_P() macro
684    
685            * R/Csparse.R (replCmat): call diagU2N() when needed
686            * R/Tsparse.R (replTmat): ditto
687    
688            * src/dtCMatrix.c (tCMatrix_validate): new
689            * src/dtTMatrix.c (tTMatrix_validate): new, used in
690            * R/AllClass.R: for validity of dtC, dsC, and dtT, dsT.
691    
692            * R/diagMatrix.R (replDiag): to use in [<-
693    
694    2006-12-22  Martin Maechler  <maechler@stat.math.ethz.ch>
695    
696            * R/Auxiliaries.R (as_Csparse2, as_geSimpl): new functions;
697                    also more general diagU2N().
698    
699    2006-12-21  Martin Maechler  <maechler@stat.math.ethz.ch>
700    
701            * R/bind2.R: new file for all cbind2(), rbind() methods moved here
702            from R/<foo>Matrix.R files. Better diagonal & improved sparse methods.
703    
704    2006-12-20  Martin Maechler  <maechler@stat.math.ethz.ch>
705    
706            * tests/bind.R: a few more cases
707            * R/Auxiliaries.R (.M.kind): also work for atomic vectors
708    
709            * R/denseMatrix.R (cbind2/rbind2): moved here (and generalized) from
710            * R/ddenseMatrix.R (cbind2/rbind2)
711            * R/Tsparse.R (replTmat): final(?!) fix for "[<-" ..
712            * tests/indexing.R
713            * tests/indexing.Rout.save: updated
714    
715    2006-12-18  Martin Maechler  <maechler@stat.math.ethz.ch>
716    
717            * R/Tsparse.R (replTmat): fixed a remaining "[<-" bug in
718            * tests/indexing.R
719    
720    2006-12-15  Martin Maechler  <maechler@stat.math.ethz.ch>
721    
722            * R/sparseMatrix.R (prSpMatrix): "." alignment much improved:
723            align with proper position of "0", i.e., right for integers.
724            argument 'align' by default is "fancy".
725    
726    2006-12-14  Martin Maechler  <maechler@stat.math.ethz.ch>
727    
728            * R/sparseMatrix.R: delegate "Compare" to "Csparse.."
729            * R/Csparse.R: and fix "Compare" for more cases.
730            * tests/Class+Meth.R: test some of these (m == m, m != m)
731    
732    2006-12-13  Martin Maechler  <maechler@stat.math.ethz.ch>
733    
734            * R/lsparseMatrix.R: all() and any() methods
735            * R/ldenseMatrix.R:      ditto
736            * NAMESPACE, R/Matrix.R: ditto
737    
738            * man/all-methods.Rd: document them minimally
739    
740            * tests/simple.R: add a few examples for these
741    
742    2006-12-11  Martin Maechler  <maechler@stat.math.ethz.ch>
743    
744            * R/Tsparse.R ([): fix long standing typo in symmetric case
745            * man/dsCMatrix-class.Rd: add example exhibiting the above case
746    
747    2006-12-10  Douglas Bates  <bates@stat.wisc.edu>
748    
749            * src/CHMfactor.c (CHMfactor_to_sparse): change LDL factorization
750            to LL before converting to a sparse matrix. (The LDL form can be
751            converted to a sparse matrix but it is implicitly a unit
752            triangular matrix and a diagonal matrix overwritten on the diagonal.)
753    
754    2006-12-09  Douglas Bates  <bates@stat.wisc.edu>
755    
756            * src/chm_common.c (chm_factor_to_SEXP): allocate and fill the Dim slot.
757    
758    2006-12-08  Douglas Bates  <bates@stat.wisc.edu>
759    
760            * DESCRIPTION (Version): updated -> release 0.9975-7
761            * src/{init.c,chm_common.c}, inst/include/*: export cholmod_analyze_p
762    
763    2006-11-30  Martin Maechler  <maechler@stat.math.ethz.ch>
764    
765            * R/diagMatrix.R (%*%): write a direct [diag o Csparse] method
766    
767    2006-11-29  Douglas Bates  <bates@stat.wisc.edu>
768    
769            * src/dgeMatrix.c (dgeMatrix_solve): Check error code from dgetri.
770            * tests/dg_Matrix.R: Add Barry Rowlingson's test of a matrix that
771            is exactly singular.
772    
773    2006-11-07  Martin Maechler  <maechler@stat.math.ethz.ch>
774    
775            * DESCRIPTION (Date): updated -> release 0.9975-6
776    
777    2006-11-06  Martin Maechler  <maechler@stat.math.ethz.ch>
778    
779            * R/Csparse.R (replCmat): symmetric indexing of symmetric matrix
780            now returns symmetric.
781    
782            * R/zzz.R ("diag<-"): replace "diag<-" in base for R <= 2.4.x
783    
784            * R/Matrix.R (.M.sub.i.2col):  new, for  M[ cbind(i,j) ] indexing.
785            * R/Matrix.R (.M.repl.i.2col): new, for  M[ cbind(i,j) ] <- value
786    
787            * R/Auxiliaries.R (.type.kind): added
788    
789    2006-11-04  Martin Maechler  <maechler@stat.math.ethz.ch>
790    
791            * src/cs.[ch]: updated to CSparse Version 2.0.3 by simply
792            running src/CSparse_install.sh
793    
794            * R/denseMatrix.R: "[": keep symmetric on symmetric indexing.
795    
796    2006-11-03  Martin Maechler  <maechler@stat.math.ethz.ch>
797    
798            * src/dsCMatrix.c (dsCMatrix_Csparse_solve): new
799            * R/dsCMatrix.R (solve): "fully-sparse" using the above.
800    
801            * R/AllClass.R: "pMatrix" now also inherits from "generalMatrix"
802    
803            * tests/Class+Meth.R (tstMatrixClass): now assure
804            the (important in method programming) property :
805    
806                    ###>>  Every "Matrix" is either
807                    ###>>  "general*", "symmetric*", "triangular*" or "diagonal*"
808    
809                    (where "*" stands for "Matrix")
810    
811            * R/Auxiliaries.R (diagU2N): now .Call()s Csparse_diagU2N for <Csparse>
812    
813            * R/dMatrix.R (Compare(<dMatrix>,<dMatrix>): update and
814            * tests/validObj.R: checks for "comparison"
815    
816            * R/sparseMatrix.R ([): improved indexing for sparse;
817                    trying to keep <symmetric>[ n, n] symmmetric
818    
819            * tests/indexing.R: indexing for logical sparse now ok
820    
821    
822    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
823    
824            * src/Tsparse.c: use xTsparse_validate() , and hence remove
825    
826            * src/{ltC,lsC,lgT}Matrix.[ch]: removed
827    
828    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
829    
830            * R/AllClass.R (Matrix-class): check length of dimnames in validity.
831    
832            * tests/simple.R: validObject() checking the above.
833    
834            * src/dgCMatrix.c (xCMatrix_validate): new, small and simple,
835            replacing both dgCMatrix_validate and lgCM*.
836    
837            * src/Csparse.c (Csparse_dense_prod, etc): do not lose dimnames;
838            fix dimnames setting in other places.
839            * src/chm_common.c (chm_dense_to_SEXP): now can pass dimnames
840    
841    2006-11-01  Martin Maechler  <maechler@stat.math.ethz.ch>
842    
843            * R/Csparse.R,src/Csparse.c, etc: tcrossprod(<CsparseM>,<CsparseM>)
844    
845            * R/sparseMatrix.R (isSymmetric): drop 'factors' slot for
846            symmetry test, via
847            * R/Auxiliaries.R (.as.dgC.0.factors):
848    
849    2006-11-01  Douglas Bates  <bates@r-project.org>
850    
851            * R/Csparse.R,src/Csparse.c,tests/matprod.R,
852            man/CsparseMatrix-class.Rd: crossprod(<CsparseMatrix>,
853            <CsparseMatrix>) added
854    
855    2006-10-30  Martin Maechler  <maechler@stat.math.ethz.ch>
856    
857            * tests/matprod.R: add a variation of Harri's example
858    
859            * R/dsparseMatrix.R: fix crossprod(<dsparse>, <dge>) to *not*
860            recursive infinitely.
861    
862            * R/dgCMatrix.R: + solve(<sparse>, <sparse>)
863    
864            * tests/indexing.R: add test for the "<" bug fixed 10-27 in R/dMatrix.R
865    
866    2006-10-28  Martin Maechler  <maechler@stat.math.ethz.ch>
867    
868            * tests/Class+Meth.R (tstMatrixClass): more: use non-trivial
869            matrix if possible; test m+m == 2*m; now test dgRMatrix.
870            * R/dgRMatrix.R (.to.dgR): a few more coercions, in order to
871            satisfy the above test.
872    
873    2006-10-27  Martin Maechler  <maechler@stat.math.ethz.ch>
874    
875            * R/Matrix.R (Ops):  <Matrix> o <matrix>  method added
876    
877            * R/dgCMatrix.R: solve(a, b="missing") based on
878            * src/dgCMatrix.c (dgCMatrix_matrix_solve): extend to work with
879            RHS = NULL.
880    
881            * R/diagMatrix.R (diagdiagprod): extend %*% etc to ldiMatrix;
882            add more (needed) [t]crossprod() methods.
883    
884            * man/ddiMatrix-class.Rd: more info, notably on 'diag'
885    
886            * R/Auxiliaries.R (as_CspClass): cleanup
887            (drop0): internal utility for "Csparse_drop(*, 0)"
888            (.bail.out.2): encourage active feedback
889    
890    2006-10-26  Martin Maechler  <maechler@stat.math.ethz.ch>
891    
892            * R/dMatrix.R(Compare): new(), then slots [no validity check]
893    
894            * src/Csparse.c (Csparse_validate): fixed (and more efficient in
895            non-valid or 'sorted' case).
896    
897            * R/dsparseMatrix.R: add "chol" method.
898            * R/ddenseMatrix.R: ditto
899    
900            * R/diagMatrix.R (Ops): group methods for  <diagonal> o <sparse>
901            * NAMESPACE (Ops)
902            * R/diagMatrix.R (diag2T): simple utility used "higher level"
903            coercion; deprecating direct lower level coercions.
904    
905            * R/*.R (seq): use seq_len() and seq_along() where possible.
906    
907    
908    2006-10-23  Martin Maechler  <maechler@stat.math.ethz.ch>
909    
910            * DESCRIPTION (Version): 0.9975-5 ready for release
911    
912    2006-10-20  Douglas Bates  <bates@stat.wisc.edu>
913    
914            * src/init.c (R_init_Matrix): export more cholmod CCallable functions.
915    
916    2006-10-20  Martin Maechler  <maechler@stat.math.ethz.ch>
917    
918            * R/AllClass.R (corMatrix): add 'validity' check;
919                    comment out unused "LDL" class definition
920            * NAMESPACE: mention, but do not export "LDL" class
921            * R/corMatrix.R: new (simple), needed for R-devel with
922            * tests/Class+Meth.R (tstMatrixClass): 1 exception for corMatrix
923              coerce and t() exceptions for all 5 'Mat.MatFact' classes.
924    
925    2006-10-19  Douglas Bates  <bates@stat.wisc.edu>
926    
927            * src/chm_common.h: Add R_cholmod_start to initialize cholmod to
928            use Rprintf and R's error handling.
929    
930    2006-10-17  Martin Maechler  <maechler@stat.math.ethz.ch>
931    
932            * R/diagMatrix.R (%*%): rep(*, each = .) in Matrix %*% diagonal.
933            * tests/matprod.R: add tests for the bug fixed.
934    
935    2006-10-11  Douglas Bates  <bates@stat.wisc.edu>
936    
937            * src/HBMM.[ch]: remove HarwellBoeing format for writing.
938            * src/SOURCES_C.mkf (SOURCES_C): no longer compile iohb.c
939    
940    2006-10-06  Douglas Bates  <bates@stat.wisc.edu>
941    
942            * R/d[gs]CMatrix.R: deprecate the writeHB function.  Use writeMM instead.
943    
944    2006-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
945    
946            * DESCRIPTION (Version): 0.9975-3
947    
948            * R/diagMatrix.R (bdiag): new function constructing block diagonal
949            (sparse) matrices.
950            * man/bdiag.Rd: docu + examples
951    
952            * R/Csparse.R (replCmat): calling new Csparse_drop() now.
953    
954            * src/Csparse.c (Csparse_general_to_symmetric, Csparse_drop): new functions
955            * R/lsCMatrix.R: three more coercions to lsC (thanks to the above)
956    
957            * R/diagMatrix.R (Diagonal): '[<-' method for diag.matrices such
958            that result is sparse or diagonal (and not dense).
959    
960            * man/Subassign-methods.Rd: fix examples
961    
962            * R/Matrix.R (Matrix):  Matrix(0, *) or Matrix(*, sparse=TRUE)
963            should always return a sparse (and not sometimes a diagonal) matrix.
964    
965    2006-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
966    
967            * R/Matrix.R ([<-): also for value "Matrix" or "matrix"
968    
969    2006-10-04  Douglas Bates  <bates@stat.wisc.edu>
970    
971            * DESCRIPTION (Version): 0.9975-2
972    
973            * inst/include/Matrix_stubs.c (M_cholmod_sparse_to_triplet): export more symbols
974    
975    2006-10-02  Douglas Bates  <bates@R-project.org>
976    
977            * tests/dg_Matrix.R: Simplify test taking into account new code.
978    
979    2006-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
980    
981            * R/Csparse.R (replCmat): improve for missing i / j in non-simple cases
982    
983            * R/lsTMatrix.R: new files w/ missing methods
984            * R/nsTMatrix.R:  "  'for completeness'
985    
986            * tests/Class+Meth.R: a bit less 'not.ok.classes'
987    
988            * R/Tsparse.R (t): generalized "t" method from "dgT*" to "Tsparse*"
989    
990    
991    2006-09-28  Douglas Bates  <bates@R-project.org>
992    
993            * src/dppMatrix.h: Ensure definition of dspMatrix_validate is
994            included.
995    
996            * src/init.c, inst/include/{Matrix.h,Matrix_stubs.h,cholmod.h}:
997            Export C-callable functions used in Zt_create in lme4.
998    
999    2006-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
1000    
1001            * DESCRIPTION (Version): 0.9975-1
1002    
1003            * tests/simple.R: less checks fail; using NA, found that our
1004                    kronecker() is not base-compatible with NA's.
1005    
1006            * R/dMatrix.R: "Compare" method now implemented for all cases
1007    
1008            * R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility
1009    
1010            * man/dtpMatrix-class.Rd: mention length of 'x' slot
1011    
1012            * src/dtpMatrix.c (dtpMatrix_validate): fix check
1013            * src/dspMatrix.c (dspMatrix_validate): ditto
1014    
1015            * R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
1016              including coercion to [nl]tTMatrix.
1017    
1018            * R/diagMatrix.R (show): print a header line as for other classes.
1019    
1020    2006-09-27  Martin Maechler  <maechler@stat.math.ethz.ch>
1021    
1022            * src/Makefile.win (SUBDIRS): fix typo
1023    
1024    2006-09-19  Martin Maechler  <maechler@stat.math.ethz.ch>
1025    
1026            * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
1027    
1028    2006-09-18  Douglas Bates  <bates@stat.wisc.edu>
1029    
1030            * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
1031            symmetric and y missing in R code using %*% (cholmod_aat doesn't
1032            accept a symmetric matrix).
1033            * tests/group-methods.R: Uncomment test of crossprod applied to
1034            lsCMatrix objects.
1035    
1036    2006-09-18  Martin Maechler  <maechler@stat.math.ethz.ch>
1037    
1038            * R/AllClass.R (symmetricMatrix): add validity method (available
1039            in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
1040    
1041            * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
1042    
1043            * tests/indexing.Rout.save:
1044            * tests/indexing.R: additions, mainly for 'lsparse'
1045    
1046            * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
1047            case.
1048    
1049            * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
1050    
1051    2006-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
1052    
1053            * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
1054                    as 'N' (1-letter - Ok?)
1055    
1056            * tests/group-methods.R: add test for logical + NAs
1057    
1058            * R/dMatrix.R ("Compare"): fix to work with NA's
1059    
1060            * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
1061    
1062            * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
1063                    which is implemented.
1064    
1065    2006-09-15  Martin Maechler  <maechler@stat.math.ethz.ch>
1066    
1067            * src/chm_common.c: coerce logical <-> double instead of
1068            typecasting;  needed for "l" matrix handling in cholmod.
1069    
1070            * tests/other-pkgs.R (graph): small extension in "graph" checks.
1071    
1072            * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
1073            (Tsp2grNEL): other fixes needed
1074    
1075    2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
1076    
1077            * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
1078                    Matrices, since "lMatrix", also "lsparseM" can have NA
1079            * R/ndenseMatrix.R, etc: new source files
1080            * man/nsparseMatrix-classes.Rd, etc: new help files
1081            * tests/: adaptions
1082            * src/chm_common.c (chm_dense_to_SEXP): and others:
1083                    new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
1084            * src/Csparse.c, etc: ditto
1085    
1086    2006-09-11  Douglas Bates  <bates@R-project.org>
1087    
1088            * src/Mutils.[ch],init.c inst/include/*.h: Move the
1089            alloc_d**Matrix functions to the lme4 package.
1090    
1091    2006-09-09  Douglas Bates  <bates@R-project.org>
1092    
1093            * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
1094            fixed
1095    
1096    2006-09-09  Martin Maechler  <maechler@stat.math.ethz.ch>
1097    
1098            * R/lMatrix.R: new
1099    
1100            * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
1101    
1102            * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
1103            * man/tcrossprod.Rd: ditto
1104    
1105    2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
1106    
1107            * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
1108            for exported functions
1109            * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
1110            Remove partitioning algorithms for sparse matrix reordering.  The
1111            copyright on the Metis code was problematic and the methods were
1112            rarely used.
1113            * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
1114            operations are now done entirely in CHOLMOD code.
1115    
1116    2006-09-06  Douglas Bates  <bates@R-project.org>
1117    
1118            * src/Mutils.h: Remove functions that are no longer used.
1119    
1120    2006-09-04  Douglas Bates  <bates@R-project.org>
1121    
1122            * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
1123            * src/DEPS.mkf: update
1124    
1125    2006-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>
1126    
1127            * created branches/Matrix-for-R-2.3.x;  on trunk: do
1128            * DESCRIPTION (Version): 0.9975-0
1129            (Depends): R (>= 2.4.0)
1130    
1131    2006-09-01  Douglas Bates  <bates@R-project.org>
1132    
1133            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
1134    
1135    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
1136    
1137            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
1138            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
1139    
1140            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
1141    
1142    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
1143    
1144            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
1145            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
1146            * R/dsparseMatrix.R: ditto
1147            * R/Csparse.R: ditto
1148    
1149    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
1150    
1151            * R/dMatrix.R (Compare): improve availability of "<", etc
1152            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
1153    
1154    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1155    
1156            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
1157            of a 0-index which was used as 1-index (..hmm)
1158    
1159            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
1160    
1161            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
1162            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
1163            (.is.diagonal): ditto
1164    
1165            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
1166    
1167            * R/Matrix.R (Matrix): also work for NA data
1168    
1169    2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
1170    
1171            * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
1172            in all cases.
1173    
1174    2006-08-27  Douglas Bates  <bates@R-project.org>
1175    
1176            * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
1177            (ddense_band): Added triu, tril and band for ddenseMatrix objects.
1178    
1179    2006-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
1180    
1181            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
1182            subclasses of "ddenseMatrix"
1183            * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
1184            * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
1185            instead of half dozen specialized ones.
1186    
1187    2006-08-25  Douglas Bates  <bates@R-project.org>
1188    
1189            * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
1190            <tillard@cirad.fr> - ordering standard errors to match effects.
1191    
1192    2006-08-24  Douglas Bates  <bates@R-project.org>
1193    
1194            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
1195            on R_ldl.
1196            * R/lCholCMatrix.R,
1197            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
1198            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
1199            * many files in ./R and ./src: Use more general version of
1200            dup_mMatrix_as_dgeMatrix to simplify method definitions.
1201            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
1202            dtpMatrix, dspMatrix and dppMatrix conversions.
1203    
1204    
1205    2006-08-23  Douglas Bates  <bates@R-project.org>
1206    
1207            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
1208            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
1209          * src/dgeMatrix.c: Ensure 'factors' slot exists in result of          * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
1210          dgeMatrix_crossprod (may need to do this in other places).          dgeMatrix_crossprod (may need to do this in other places).
1211          * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky          * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky

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