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revision 1548, Mon Sep 11 22:13:07 2006 UTC revision 2073, Wed Sep 26 16:17:00 2007 UTC
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1    2007-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * R/pMatrix.R (.m.mult.pMat): fix <matrix> %*% <pMatrix>,
4              thanks to Kasper Kristensen.
5            * tests/matprod.R: regression test for that.
6    
7    2007-09-23 17:32  Douglas Bates <bates@stat.wisc.edu>
8    
9            * [r4778] R/AllGeneric.R: Check R version before defining generics for
10              primitives
11    
12    2007-09-13  Martin Maechler  <maechler@stat.math.ethz.ch>
13    
14            * R/denseMatrix.R (rcond): method
15            * R/sparseQR.R (rcond): method, use x or t(x)
16    
17    2007-09-12  Martin Maechler  <maechler@stat.math.ethz.ch>
18    
19            * R/dgeMatrix.R (rcond): method: work via qr.R() for non-square
20            matrices.
21            * R/sparseMatrix.R: Ditto for all other rcond() method definitions.
22    
23            * man/rcond.Rd: mention the more general definition, and add
24            example for non-square matrices.
25    
26            * man/chol.Rd: new file, for the S4 chol() generic and all methods.
27    
28    2007-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
29    
30            * R/sparseQR.R: add qr.R() method [to be used for rcond()]
31    
32    2007-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
33    
34            * R/Matrix.R ([<-): add (Matrix,missing,ANY,Matrix) etc
35            * tests/indexing.R: add new regression for the above cases.
36    
37    2007-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
38    
39            * src/Mutils.h (__sun): clause for alloca.h on Solaris
40    
41    2007-08-16  Martin Maechler  <maechler@stat.math.ethz.ch>
42    
43            * DESCRIPTION (Date, Version): 0.999375-2
44    
45    2007-08-15  Martin Maechler  <maechler@stat.math.ethz.ch>
46    
47            * R/HBMM.R (readMM): make work for pattern matrices as well
48    
49    2007-08-14 13:07  Douglas Bates <bates@stat.wisc.edu>
50    
51            * [r4730] src/Mutils.h: declare alloca
52            * [r4734] NAMESPACE, R/AllGeneric.R, R/Csparse.R, R/HBMM.R, R/Tsparse.R,
53              R/dgCMatrix.R, R/dgTMatrix.R, R/dsCMatrix.R, R/dsTMatrix.R,
54              man/externalFormats.Rd, src/Csparse.c, src/Csparse.h, src/DEPS.mkf,
55              src/HBMM.c, src/HBMM.h, src/Mutils.h, src/SOURCES_C.mkf, src/init.c,
56              src/mmio.c, src/mmio.h: Remove deprecated function writeHB and its
57              methods; switch writeMM to use CHOLMOD code; repair readMM
58    
59    2007-08-14  Martin Maechler  <maechler@stat.math.ethz.ch>
60    
61            * R/nearPD.R, man/nearPD.Rd (nearPD): new function built on Jens
62            Oehlschlaegel's ... result type still to be discussed!
63    
64    2007-08-10  Martin Maechler  <maechler@stat.math.ethz.ch>
65    
66            * man/image-methods.Rd: new, combining all image() methods
67    
68    2007-08-09  Martin Maechler  <maechler@stat.math.ethz.ch>
69    
70            * R/dgCMatrix.R: define qr() and lu() methods for "sparseMatrix"
71            to work via dgC...
72    
73            * R/Matrix.R (Matrix): special treatment for "table" (S3)
74    
75    2007-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
76    
77            * R/dgTMatrix.R (image): change defaults to
78                    aspect = "iso", colorkey = FALSE
79    
80    2007-08-06  Martin Maechler  <maechler@stat.math.ethz.ch>
81    
82            * src/dsyMatrix.c (dsyMatrix_matrix_mm): 'b' might be matrix;
83            must copy its *expanded* x slot before LAPACK call.
84    
85            * tests/matprod.R: test the last days' changes.
86    
87    2007-08-06 16:43  Douglas Bates <bates@stat.wisc.edu>
88    
89            * [r4712] inst/include/Matrix_stubs.c: Change R_cholmod_printf in stubs
90              as well as in sources
91            * [r4713] src/dsyMatrix.c: Duplicate the contents of the RHS before
92              Lapack call
93    
94    2007-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
95    
96            * R/Matrix.R (%*%, crossprod, tcrossprod): add method for
97                    ("Matrix", "matrix") which is needed in some cases.
98            Ditto for solve().
99    
100            * R/colSums.R (.as.dge.Fun): need ddenseMatrix methods to avoid
101            infinite recursion in dispatch for some cases.
102    
103    2007-08-02 08:48  Martin Maechler <maechler@stat.math.ethz.ch>
104    
105            * [r4693] src/chm_common.c: R_cholmod_printf() instead of Rprintf() just
106              so pointers match
107    
108    2007-08-02  Martin Maechler  <maechler@stat.math.ethz.ch>
109    
110            * DESCRIPTION (Date): set ready for release -- 0.999375-1
111    
112    2007-08-01 15:44  Douglas Bates <bates@stat.wisc.edu>
113    
114            * [r4686] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
115              src/chm_common.c, src/chm_common.h: Change API for
116              numeric_as_chm_dense and N_AS_CHM_DN
117    
118    2007-08-01  Martin Maechler  <maechler@stat.math.ethz.ch>
119    
120            * src/dtrMatrix.c (dtrMatrix_matrix_mm): fix dimensionality check (!)
121            * tests/matprod.R: regr.test for it
122    
123    2007-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
124    
125            * R/dMatrix.R: fix from Brian for   Math2(., digits = "missing")
126            * tests/group-methods.R: and regression-test it
127    
128    2007-07-19 19:45  Douglas Bates <bates@stat.wisc.edu>
129    
130            * [r4642] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
131              inst/include/cholmod.h, src/chm_common.c, src/init.c: Export
132              triplet_to_sparse, documentation, use typedefs
133    
134    2007-07-18  Martin Maechler  <maechler@stat.math.ethz.ch>
135    
136            * man/dpoMatrix-class.Rd: added 'corMatrix' example
137    
138            * src/dsyMatrix.[ch] (dsyMatrix_as_matrix): new 'keep_dimnames' arg
139            * src/dtrMatrix.[ch] (dtrMatrix_as_matrix): ditto
140            * src/init.c, R/dsyMatrix.R, R/dtrMatrix.R, R/lgTMatrix.R: ditto
141    
142            * R/lsparseMatrix.R: bug fix in "all" method
143            * R/Ops.R (.do.Logic.lsparse): "|" bug in borderline case
144    
145            * R/dsyMatrix.R (coerce->dsTMatrix): (i,j) slots should *not* have names
146            * R/ngTMatrix.R (coerce->ngTMatrix): ditto;
147                    + matrix |-> nMatrix coercion
148            * R/pMatrix.R: + setAs()  to dMatrix and from nMatrix
149            * man/pMatrix-class.Rd: ditto
150    
151            * R/Matrix.R (Summary): method for non-dMatrix
152    
153            * tests/Class+Meth.R (extraValid): new check about "dirty" slots
154            * tests/Class+Meth.R (tstMatrixClass): test norm(.);
155                    test all Summary methods.
156    
157    2007-07-16  Martin Maechler  <maechler@stat.math.ethz.ch>
158    
159            * R/dgeMatrix.R (norm, rcond): methods for 'matrix'
160    
161    2007-07-14  Martin Maechler  <maechler@stat.math.ethz.ch>
162    
163            * R/sparseMatrix.R (norm): simple methods for sparseMatrix
164    
165            * R/pMatrix.R (t?crossprod): methods for pMatrix
166    
167    2007-07-10  Douglas Bates  <bates@stat.wisc.edu>
168    
169            * src/dgeMatrix.c (dgeMatrix_colsums): Get the logic straight.
170    
171    2007-07-09 20:45  Douglas Bates <bates@stat.wisc.edu>
172    
173            * [r4579] src/dgeMatrix.c: Untangle horrible code in dgeMatrix_colsums
174              trying to fix a subtle bug - which has been somewhere else.
175    
176    2007-07-09 19:43  Martin Maechler <maechler@stat.math.ethz.ch>
177    
178            * [r4578] src/dgeMatrix.c: "cleaned" dgeMatrix_colsums() - but did not
179              solve the bug
180    
181    2007-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
182    
183            * src/dgCMatrix.c (compressed_to_TMatrix):
184    
185    2007-07-07  Martin Maechler  <maechler@stat.math.ethz.ch>
186    
187            * src/Csparse.c (Rsparse_validate): new, to have some validity
188            checking for RsparseMatrix
189            * src/dgCMatrix.c (xRMatrix_validate): ditto
190            * src/dtCMatrix.c (tRMatrix_validate): ditto
191    
192    2007-07-07  Douglas Bates <bates@stat.wisc.edu>
193    
194            * [r4567] R/AllClass.R: Slots already in RsparseMatrix were redefined in
195              lgRMatrix
196            * [r4568] DESCRIPTION: Prepare for bug-fix release
197            * [r4570] src/CHOLMOD/Check/cholmod_write.c: Include cholmod_matrixops.h
198              for declaration of cholmod_symmetry
199    
200    2007-07-06  Martin Maechler  <maechler@stat.math.ethz.ch>
201    
202            * DESCRIPTION (Version): 0.999375 merged into the trunk; ready for
203            release.
204    
205    2007-07-06 14:11  Douglas Bates <bates@stat.wisc.edu>
206    
207            * [r4559] src/iohb.c, src/iohb.h: Remove Harwell-Boeing input/output
208              functions - no longer used
209            * [r4560] src/HBMM.c, src/Mutils.c, src/dgTMatrix.c, src/dgeMatrix.c,
210              src/dspMatrix.c, src/dsyMatrix.c, src/dtCMatrix.c,
211              src/factorizations.c, src/sparseQR.c: Replace most calls to Calloc by
212              Alloca
213    
214    2007-07-06 13:14  Martin Maechler <maechler@stat.math.ethz.ch>
215    
216            * [r4558] inst/doc/Comparisons.Rnw, src/CHMfactor.c, src/Csparse.c,
217              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dense.c,
218              src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c, src/sparseQR.c,
219              src/t_gCMatrix_colSums.c: more R_CheckStack()s
220    
221    2007-07-05 18:12  Douglas Bates <bates@stat.wisc.edu>
222    
223            * [r4550] inst/include/Matrix.h: Add the macro N_AS_CHM_DN to "alloca"
224              the required amount of memory then call M_numeric_as_chm_dense.
225            * [r4556] src/Mutils.h, src/dgCMatrix.c: Define and use the Alloca macro
226              (like Calloc but calling alloca)
227    
228    2007-07-05  Martin Maechler  <maechler@stat.math.ethz.ch>
229    
230            * R/sparseMatrix.R (printSpMatrix): renamed from prSpMatrix()
231            and extended with more sophisticated 'col.names' option.
232            * NAMESPACE: export  printSparseMatrix()
233            * man/printSpMatrix.Rd: document, incl. examples
234    
235    2007-07-04 16:21  Douglas Bates <bates@stat.wisc.edu>
236    
237            * [r4543] src/cs_utils.c, src/cs_utils.h, src/dgCMatrix.c,
238              src/dtCMatrix.c, src/sparseQR.c: CSP typedef for *cs and macro
239              AS_CSP. API change - pass the empty structure to Matrix_as_cs.
240    
241    2007-07-04  Martin Maechler  <maechler@stat.math.ethz.ch>
242    
243            * DESCRIPTION (Version): 0.99875-4
244    
245            * tests/Class+Meth.R (tstMatrixClass): add dimnames, and hence test
246            some dimnames perservation.
247    
248            * R/dsTMatrix.R (t-method): keep dimnames
249            * R/dtTMatrix.R:  ditto
250    
251            * R/sparseMatrix.R (prSpMatrix): print colnames when non-trivial
252            and ncol(.) < 10
253    
254            * src/cs_utils.c: drop check_class() and use Matrix_check_class()
255            from Mutils.h
256    
257            * src/lgCMatrix.c ([ln]csc_to_matrix): no longer lose dimnames,
258            e.g. in as(<ngCMatrix>, "matrix")
259    
260    2007-07-01 13:27  Douglas Bates <bates@stat.wisc.edu>
261    
262            * [r4529] .: Create a branch for the API changes from the 0.99875
263              series to the 0.999375 series
264            * [r4530] DESCRIPTION, inst/include/Matrix.h,
265              inst/include/Matrix_stubs.c, src/CHMfactor.c, src/Csparse.c,
266              src/Mutils.h, src/Tsparse.c, src/chm_common.c, src/chm_common.h,
267              src/dense.c, src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c,
268              src/t_gCMatrix_colSums.c: API change - pass the empty structure to the
269              as_cholmod_x functions
270    
271    2007-06-30 09:05  Martin Maechler <maechler@stat.math.ethz.ch>
272    
273            * [r4527] trunk/Matrix/DESCRIPTION, trunk/Matrix/NAMESPACE,
274              trunk/Matrix/inst/doc/Comparisons.Rnw: add session- and hardware-info
275              to Comparisons
276    
277    >>>>>>> .merge-right.r4561
278    2007-06-29  Martin Maechler  <maechler@stat.math.ethz.ch>
279    
280            * DESCRIPTION (Version): 0.99875-3 ready to be released.
281    
282            * R/sparseMatrix.R (spMatrix): make spMatrix(3,4) working
283    
284            * R/AllGeneric.R: set "Math" (and "Math2") group generics in a way
285            that should also work in a future version of R.
286    
287    2007-06-21  Martin Maechler  <maechler@stat.math.ethz.ch>
288    
289            * NAMESPACE, R/AllClass.R: "xsparseVector" class union.
290    
291            * R/sparseVector.R: more *sparseVector coercions, notably for
292            non - double ones.
293    
294    2007-06-19  Martin Maechler  <maechler@stat.math.ethz.ch>
295    
296            * R/colSums.R: new file for all (col|row)(Sums|Means) methods,
297              notably the new ones building on the new .Call(.)s:
298    
299            * src/dgCMatrix.c (DEF_gCMatrix_COLSUMS): use to define
300            all 4 of [dlin]gCMatrix_colSums().
301    
302    2007-06-18 16:12  Douglas Bates <bates@stat.wisc.edu>
303    
304            * [r4472] src/Syms.h, src/init.c: Added Matrix_lengthSym
305            * [r4473] src/dgCMatrix.c: Modified dgCMatrix_colSums for sparseVector
306              result
307    
308    2007-06-16  Martin Maechler  <maechler@stat.math.ethz.ch>
309    
310            * R/kronecker.R: fix typo (could lead to inf.recursion)
311            * test/simple.R: testing that
312    
313            * R/sparseMatrix.R (prSpMatrix): change to be used as print()
314            method as well (which can have arguments, show() can't).
315    
316    2007-06-16 15:52  Douglas Bates <bates@stat.wisc.edu>
317    
318            * [r4466] R/dgCMatrix.R, src/dgCMatrix.c, src/dgCMatrix.h, src/init.c:
319              added dgCMatrix_colSums for [col,row][Sums,Means]
320    
321    2007-06-15 23:15  Douglas Bates <bates@stat.wisc.edu>
322    
323            * [r4460] R/sparseMatrix.R, man/dgCMatrix-class.Rd, src/dgCMatrix.c,
324              src/dgCMatrix.h, src/init.c: added lm.fit.sparse (unexported),
325              coercion of "factor" to "dgCMatrix" and dgCMatrix_cholsol
326            * [r4461] R/AllClass.R, man/sparseMatrix-class.Rd: draft "indicators"
327              class
328            * [r4463] R/sparseMatrix.R, man/dgCMatrix-class.Rd,
329              man/sparseMatrix-class.Rd: Don't need an "indicators" class - use the
330              row names to store the levels - duh!  Added an example.
331    
332    2007-06-14  Martin Maechler  <maechler@stat.math.ethz.ch>
333    
334            * src/Csparse.c (Csparse_validate): check for *repeated* entries
335            thanks to example from Christian Buchta; with a test here:
336            * tests/simple.R:
337    
338    2007-06-07  Martin Maechler  <maechler@stat.math.ethz.ch>
339    
340            * R/Auxiliaries.R (callGeneric): another fix, needed for some cases
341            of colSums(*, sparseResult = TRUE)
342    
343    2007-06-06  Martin Maechler  <maechler@stat.math.ethz.ch>
344    
345            * R/lsparseMatrix.R, R/ldenseMatrix.R (all, any): change default to
346            'na.rm = FALSE' as "everywhere" else in R.
347    
348    2007-06-05 Douglas Bates <bates@stat.wisc.edu>
349    
350            * [r4421] src/CSparse_install.sh: Modify for new organization of
351              CSparse package
352            * [r4425] src/UFsparse_download.sh: Update to version 3.0.0 of
353              SuiteSparse
354            * [r4426] src/Makefile: add ./UFconfig to the include path for
355              compilation
356            * [r4427] src/cs.[ch]: update to CSparse version 2.2.0
357            * [r4428] inst/doc/UFsparse/* src/{AMD,CHOLMOD,COLAMD}/*
358              src/UFconfig/UFconfig.h: Update to version 3.0.0 of SuiteSparse
359    
360    2007-06-05  Martin Maechler  <maechler@stat.math.ethz.ch>
361    
362            * R/Auxiliaries.R (emptyColnames): + argument msg.if.not.empty, used in
363            * R/sparseMatrix.R (prSpMatrix): now gives a message about
364            suppressed column names.
365    
366    2007-06-04 17:13  Douglas Bates <bates@stat.wisc.edu>
367    
368            * [r4418] src/Csparse.c, src/HBMM.c, src/Mutils.c, src/Mutils.h,
369              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dgCMatrix.c,
370              src/dgeMatrix.c, src/dpoMatrix.c, src/dpoMatrix.h, src/dppMatrix.c,
371              src/dppMatrix.h, src/dsCMatrix.c, src/dspMatrix.c, src/dspMatrix.h,
372              src/dsyMatrix.c, src/dsyMatrix.h, src/dtpMatrix.c, src/dtrMatrix.c:
373              Remove warnings after change to const char* CHAR
374    
375    2007-06-04 17:11  Douglas Bates <bates@stat.wisc.edu>
376    
377            * [r4417] inst/include/Matrix_stubs.c, inst/include/cholmod.h: Corrected
378              type of M_cholmod_ssmult
379    
380    2007-06-03 14:42  Douglas Bates <bates@stat.wisc.edu>
381    
382            * [r4412] inst/include/Matrix_stubs.c, inst/include/cholmod.h,
383              src/init.c: Yet another cholmod export - cholmod_ssmult
384    
385    2007-05-23  Martin Maechler  <maechler@stat.math.ethz.ch>
386    
387            * NAMESPACE: exported drop0(), since
388            * man/drop0.Rd: I have seen several cases, I really wanted to use
389            it, so our users may want too.
390    
391    2007-05-22  Martin Maechler  <maechler@stat.math.ethz.ch>
392    
393            * man/colSums.Rd: separately document colSums() etc, since these
394            have the extra argument 'sparseResult'.
395    
396    2007-05-21  Martin Maechler  <maechler@stat.math.ethz.ch>
397    
398            * R/sparseMatrix.R (spMatrix): utility (T)sparse Matrix constructor;
399            * man/spMatrix.Rd: docu., including examples
400    
401            * R/Auxiliaries.R (sp.colMeans): etc, using a patched callGeneric(),
402            in order to make colMeans() etc fast *and* correct.
403            * R/sparseVector.R (replSPvec): "[<-" functionality for
404            sparseVectors; tested in
405            * tests/simple.R:
406    
407    2007-05-19  Martin Maechler  <maechler@stat.math.ethz.ch>
408    
409            * R/sparseMatrix.R (print.sparseSummary): and summary() method for
410            (very) sparse Matrices; output similar to Matlab's print().
411    
412    2007-05-17  Douglas Bates  <bates@stat.wisc.edu>
413    
414            * src/HBMM.c (Matrix_writeMatrixMarket): Write 1-based, not
415            0-based, indices (Jose Quesada <quesada@gmail.com>).
416    
417    2007-05-16  Douglas Bates  <bates@stat.wisc.edu>
418    
419            * R/CHMfactor.R: Added solve methods for a CHMfactor object.
420    
421    2007-05-16  Martin Maechler  <maechler@stat.math.ethz.ch>
422    
423            * R/Auxiliaries.R (sparsapply): new utility, much faster than
424            tapply1() for large sparse matrices.
425    
426    2007-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
427    
428            * R/Matrix.R (dim<-): reshape now via sparseVector.
429    
430            * R/sparseVector.R: methods and function for
431            * R/AllClass.R: new "sparseVector" class and daughters.
432            * NAMESPACE: export new classes
433    
434    2007-05-14  Martin Maechler  <maechler@stat.math.ethz.ch>
435    
436            * DESCRIPTION (Version): 0.99875-1
437            * src/Makefile.win: also remove Lapack code from here (cf. 04-25).
438    
439    2007-05-11  Martin Maechler  <maechler@stat.math.ethz.ch>
440    
441            * R/Tsparse.R ([, Tsparse): fix last case: *duplicated*, symmetric
442            indexing
443            * tests/indexing.R: test set for that.
444    
445    2007-05-08  Martin Maechler  <maechler@stat.math.ethz.ch>
446    
447            * R/Tsparse.R (replTmat): fix the case of *duplicated* index
448            entries.
449            * tests/indexing.R(out): add regression test for it
450    
451    2007-04-30  Martin Maechler  <maechler@stat.math.ethz.ch>
452    
453            * R/(l(dense|sparse))?Matrix.R (!): use 'x', not 'e1' as argument
454            name for "!" method definitions.
455    
456    2007-04-26  Martin Maechler  <maechler@stat.math.ethz.ch>
457    
458            * R/Tsparse.R (intI): new utility, used for "[" :
459                    Cleanup up there, and fixes for duplicated indices - more TODO!
460    
461            * tests/indexing.R(out): more tests
462    
463    2007-04-25  Douglas Bates  <bates@stat.wisc.edu>
464    
465            * DESCRIPTION,src/Makefile: require R>= 2.5.0 and remove Lapack
466            code that is now part of the R Lapack library.
467    
468            * src/init.c,inst/include/{Matrix_stubs.c,cholmod.h}:export
469            cholmod_factorize_p (used in lme4 for GLMMs and NLMMs).
470    
471    2007-04-21  Martin Maechler  <maechler@stat.math.ethz.ch>
472    
473            * R/Matrix.R (image): method for all Matrices, not just sparse ones.
474    
475    2007-04-17  Martin Maechler  <maechler@stat.math.ethz.ch>
476    
477            * R/Auxiliaries.R (tapply1): unname(.) -> colSums() etc don't end
478            up with extraneous names '0'...'<n-1>'
479    
480    2007-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
481    
482            * R/dgTMatrix.R (mat2dgT): care about NAs
483    
484    2007-04-11  Martin Maechler  <maechler@stat.math.ethz.ch>
485    
486            * R/kronecker.R: triangularity preserving methods
487    
488    2007-03-27  Martin Maechler  <maechler@stat.math.ethz.ch>
489    
490            * R/kronecker.R: new file collecting kronecker() methods in one
491                    place.  Goal: become much faster!
492    
493    2007-03-23  Martin Maechler  <maechler@stat.math.ethz.ch>
494    
495            * src/dtCMatrix.c (dtCMatrix_solve): use the new code from Kasper
496            Kristensen based cs_spsolve() instead of _lsolve & _usolve which
497            can be much faster.
498    
499            * tests/matprod.R: add regression tests for these (upper & lower).
500    
501    2007-03-19  Martin Maechler  <maechler@stat.math.ethz.ch>
502    
503            * R/Matrix.R (diff): method for our Matrices.
504    
505            * R/sparseMatrix.R (isDiagonal): check dim()!
506    
507    2007-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
508    
509            * R/Matrix.R (dim<-): new method for "reshape()" built on a
510            proposal from Tamas Papp.
511    
512    2007-03-16  Martin Maechler  <maechler@stat.math.ethz.ch>
513    
514            * R/AllGeneric.R: remove all  if(!isGeneric(.))  clauses
515    
516            * R/zzz.R (.onLoad, .onUnload): do *not* leave bind_activation(TRUE);
517            rather define and export  cBind() and rBind() only.
518            --> useRs *must* change code that used to have cbind()/rbind() !!
519    
520            * R/bind.R: change tests from cbind() to cBind() and similarly to rBind()
521            * R/bind.Rout.save: ditto
522    
523    2007-02-16  Douglas Bates  <bates@r-project.org>
524    
525            * DESCRIPTION (Date, Version): 0.9975-11 with new date
526            * src/dgCMatrix.c (R_to_CMatrix, compressed_to_TMatrix): remove
527            const modifier on declaration of the array 'valid'
528    
529    2007-02-12  Douglas Bates  <bates@stat.wisc.edu>
530    
531            * R/CHMfactor.R: Add image method (coercion to sparseMatrix).
532    
533    2007-02-05  Martin Maechler  <maechler@stat.math.ethz.ch>
534    
535            * DESCRIPTION (Date, Version): 0.9975-10 with new date.
536    
537            * R/Ops.R (Arith): make sure Csparse o Csparse also works for e.g. ntCMatrix
538            * tests/simple.R: test the above and some of these coercions:
539    
540            * R/nsparseMatrix.R: coercing "Csparse" to "lsparseMatrix";
541                    be careful to avoid infinite recursion, using new coercions in
542            * R/ngCMatrix.R and nsC... and ntC...
543            * R/lsparseMatrix.R: ditto
544    
545            * R/SparseM-conv.R: more conversion, notably for triplet matrices.
546    
547            * src/dgCMatrix.c (R_to_C_Matrix): port Doug's fix and
548            * R/Rsparse.R: reactivate .Call()s
549    
550            * tests/Class+Meth.R: a bit more on actual classes
551    
552    2007-02-04  Douglas Bates  <bates@stat.wisc.edu>
553    
554            * src/dgCMatrix.c (compressed_to_TMatrix): fix memory bug using strdup()
555    
556    2007-02-03  Martin Maechler  <maechler@stat.math.ethz.ch>
557    
558            * DESCRIPTION (Version): 0.9975-10 to upload
559    
560            * tests/Class+Meth.R (tstMatrixClass): require coercions to
561            specific classes less unconditionally.
562    
563            * R/Auxiliaries.R: get rid of as_Tsparse() and as_Rsparse()
564    
565            * R/Tsparse.R (triu): etc, use as(*, "TsparseMatrix") instead of as_Tsparse()
566    
567            * R/Rsparse.R (.R.2.T): R-level workaround using compressed_to_TMatrix.
568            * R/Rsparse.R (.R.2.C): R-level workaround since C-level
569            R_to_CMatrix segfaults on one platform.
570            Eliminate most coercion method to *specific* classes, and replace
571            with virtual classes coercions.
572    
573    
574    2007-02-01  Martin Maechler <maechler@stat.math.ethz.ch>
575    
576            * src/init.c: export the CHM...._validate() placeholders, since
577            they *are* called.
578    
579            * tests/Class+Meth.R (classCanCoerce): and starting to test
580            all as(<from>, <to>)
581    
582    2007-01-30  Martin Maechler  <maechler@stat.math.ethz.ch>
583    
584            * R/Tsparse.R ([): more care when subsetting triangular Tsparse
585            * tests/indexing.R: tested now
586            * tests/indexing.Rout.save: updated
587    
588            * src/Csparse.c (Csparse_to_dense): use Rkind = -1 for PATTERN to
589            * src/chm_common.c (chm_dense_to_SEXP): return "ngeMatrix" when
590            appropriate.
591    
592            * NAMESPACE: export a trivial
593            * R/Matrix.R: drop() Matrix-method
594    
595            * R/AllClass.R: moved all prototypes to virtual super classes.
596    
597            * R/Rsparse.R: many more coercions to have less exceptions in
598            * tests/Class+Meth.R:
599    
600            * R/Ops.R (Compare): tweak for case with NA
601            * tests/simpl.R: hence another 'FIXME' eliminated
602    
603    2007-01-29  Martin Maechler  <maechler@stat.math.ethz.ch>
604    
605            * R/diagMatrix.R (solve): the obvious methods for diagonalMatrix
606            objects.
607    
608            * tests/Class+Meth.R (tstMatrixClass): now testing diag(), nnzero(),
609              and more of "!", "&", "|", all, any; coercions
610    
611            * R/Rsparse.R: many coercions (which enable quite a few other
612            methods), thanks to enhancements in
613            * src/dgCMatrix.c (R_to_CMatrix): new, and
614            * src/dgCMatrix.c (compressed_to_TMatrix): now for (d,l,n) ,
615            symmetric & triangular and ..RMatrix objects.
616    
617            * src/TMatrix_as.c (Matrix_T_as_DENSE,Matrix_T_as_GENERAL):
618            renamed file from src/dsTMatrix.c;
619            now dealing with symmetric and triangular Tsparse coercions, both
620            to dense and general.
621    
622    2007-01-27  Martin Maechler  <maechler@stat.math.ethz.ch>
623    
624            * src/dsTMatrix.c: has now "l" and "n" methods besides the "d" ones.
625    
626            * R/Ops.R (Arith): <dgCMatrix> o <numeric> now remains sparse
627            where sensible when the <numeric> is of length > 1.
628    
629    2007-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
630    
631            * R/Matrix.R ([<-): for M[] <- value: fix length
632    
633    2007-01-25  Martin Maechler  <maechler@stat.math.ethz.ch>
634    
635            * R/Auxiliaries.R (n2l_Matrix): new, to be used in
636            * R/ndenseMatrix.R: new coercions n* -> l*
637    
638    2007-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
639    
640            * R/triangularMatrix.R: new file; simple triu() and tril() methods.
641    
642            * R/Ops.R ("Logic"): and other "Ops", many updates
643    
644    2007-01-18  Martin Maechler  <maechler@stat.math.ethz.ch>
645    
646            * src/Mutils.h (SET_DimNames): new utility
647    
648            * R/Auxiliaries.R (nnzero): improved and now exported via
649    
650            * NAMESPACE: + nnzero(); length() == prod(dim(.)) method for all "Matrix" objects
651    
652    2007-01-17  Martin Maechler  <maechler@stat.math.ethz.ch>
653    
654            * R/diagMatrix.R (!): fix typo.
655    
656    2007-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
657    
658            * R/Auxiliaries.R (as_Csparse): and quite a few others:
659                    allow to pass class definition --> speedup
660            * R/sparseMatrix.R: apply the above
661    
662            * R/Csparse.R: coercion Csparse* to dense* now preserves shape properties.
663    
664            * src/Mutils.h (mMatrix_as_geMatrix): new, based on
665            * src/Mutils.c (dup_mMatrix_as_geMatrix): new; generalization of
666            old dup_mMatrix_as_dgeMatrix), eliminating a long-standing "FIXME".
667    
668            * src/dense.c (dense_to_Csparse): use new mMatrix_as_geMatrix()
669    
670            * R/denseMatrix.R (.dense2C): based on dense_to_Csparse: name it,
671            and use it for "sparse*" as well, since it's faster than the
672            as_Csparse(.) way.
673    
674    2007-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
675    
676            * R/Ops.R ("Logic"): more methods, notably an  <lgC> o <lgC> one.
677    
678    2007-01-12  Martin Maechler  <maechler@stat.math.ethz.ch>
679    
680            * R/Tsparse.R (.TM.repl.i.2col): new internal function to be used
681            as method for   M[ ij ] <- v
682            * R/Csparse.R:: go via Tsparse for "M[ij] <- v"
683    
684            * R/Ops.R: "Compare" for (C|R)sparse: need pointer slot for all
685            FALSE answer
686    
687            * R/Csparse.R (replCmat): fix the "all non-zero" case with reordering
688            * tests/indexing.R: test it, and some of the above
689    
690    2007-01-05  Martin Maechler  <maechler@stat.math.ethz.ch>
691    
692            * R/Auxiliaries.R (is_duplicatedT): new utility
693    
694    2007-01-05  Douglas Bates  <bates@stat.wisc.edu>
695    
696            * src/init.c (R_init_Matrix): export cholmod_scale
697    
698    2006-12-30  Martin Maechler  <maechler@stat.math.ethz.ch>
699    
700            * R/zzz.R (tmp): for R >= 2.5.0, extend formals of our
701            base::as.matrix to (x, ...)
702    
703    2006-12-28  Martin Maechler  <maechler@stat.math.ethz.ch>
704    
705            * R/Ops.R ("Arith" etc): move almost all "Ops" methods to new R
706            file; start using "Logic", hence
707    
708            * DESCRIPTION (Depends): R >= 2.4.1 (since we want "Logic")
709            * NAMESPACE: import and export "Logic"
710    
711    2006-12-27  Martin Maechler  <maechler@stat.math.ethz.ch>
712    
713            * src/zpotfr.f and dependencies: use LAPACK 3.1 version
714            only needed previously to R version 2.5.0.
715    
716    2006-12-26  Martin Maechler  <maechler@stat.math.ethz.ch>
717    
718            * DESCRIPTION (Date, Version): 0.9975-8, ready for release
719    
720            * R/Tsparse.R (replTmat): fix subassignment of triangular
721            * R/Csparse.R (replCmat): ditto
722            * tests/indexing.R: more tests, incl the above fix
723    
724    2006-12-23  Martin Maechler  <maechler@stat.math.ethz.ch>
725    
726            * R/Auxiliaries.R (drop0): extend for non CSparse
727            * R/Auxiliaries.R (diagU2N): should work for all sparseMatrix
728    
729            * src/Csparse.c (Csparse_to_Tsparse, Csparse_general_to_symmetric):
730                    use uplo correctly (!); other places: use uplo_P() macro
731    
732            * R/Csparse.R (replCmat): call diagU2N() when needed
733            * R/Tsparse.R (replTmat): ditto
734    
735            * src/dtCMatrix.c (tCMatrix_validate): new
736            * src/dtTMatrix.c (tTMatrix_validate): new, used in
737            * R/AllClass.R: for validity of dtC, dsC, and dtT, dsT.
738    
739            * R/diagMatrix.R (replDiag): to use in [<-
740    
741    2006-12-22  Martin Maechler  <maechler@stat.math.ethz.ch>
742    
743            * R/Auxiliaries.R (as_Csparse2, as_geSimpl): new functions;
744                    also more general diagU2N().
745    
746    2006-12-21  Martin Maechler  <maechler@stat.math.ethz.ch>
747    
748            * R/bind2.R: new file for all cbind2(), rbind() methods moved here
749            from R/<foo>Matrix.R files. Better diagonal & improved sparse methods.
750    
751    2006-12-20  Martin Maechler  <maechler@stat.math.ethz.ch>
752    
753            * tests/bind.R: a few more cases
754            * R/Auxiliaries.R (.M.kind): also work for atomic vectors
755    
756            * R/denseMatrix.R (cbind2/rbind2): moved here (and generalized) from
757            * R/ddenseMatrix.R (cbind2/rbind2)
758            * R/Tsparse.R (replTmat): final(?!) fix for "[<-" ..
759            * tests/indexing.R
760            * tests/indexing.Rout.save: updated
761    
762    2006-12-18  Martin Maechler  <maechler@stat.math.ethz.ch>
763    
764            * R/Tsparse.R (replTmat): fixed a remaining "[<-" bug in
765            * tests/indexing.R
766    
767    2006-12-15  Martin Maechler  <maechler@stat.math.ethz.ch>
768    
769            * R/sparseMatrix.R (prSpMatrix): "." alignment much improved:
770            align with proper position of "0", i.e., right for integers.
771            argument 'align' by default is "fancy".
772    
773    2006-12-14  Martin Maechler  <maechler@stat.math.ethz.ch>
774    
775            * R/sparseMatrix.R: delegate "Compare" to "Csparse.."
776            * R/Csparse.R: and fix "Compare" for more cases.
777            * tests/Class+Meth.R: test some of these (m == m, m != m)
778    
779    2006-12-13  Martin Maechler  <maechler@stat.math.ethz.ch>
780    
781            * R/lsparseMatrix.R: all() and any() methods
782            * R/ldenseMatrix.R:      ditto
783            * NAMESPACE, R/Matrix.R: ditto
784    
785            * man/all-methods.Rd: document them minimally
786    
787            * tests/simple.R: add a few examples for these
788    
789    2006-12-11  Martin Maechler  <maechler@stat.math.ethz.ch>
790    
791            * R/Tsparse.R ([): fix long standing typo in symmetric case
792            * man/dsCMatrix-class.Rd: add example exhibiting the above case
793    
794    2006-12-10  Douglas Bates  <bates@stat.wisc.edu>
795    
796            * src/CHMfactor.c (CHMfactor_to_sparse): change LDL factorization
797            to LL before converting to a sparse matrix. (The LDL form can be
798            converted to a sparse matrix but it is implicitly a unit
799            triangular matrix and a diagonal matrix overwritten on the diagonal.)
800    
801    2006-12-09  Douglas Bates  <bates@stat.wisc.edu>
802    
803            * src/chm_common.c (chm_factor_to_SEXP): allocate and fill the Dim slot.
804    
805    2006-12-08  Douglas Bates  <bates@stat.wisc.edu>
806    
807            * DESCRIPTION (Version): updated -> release 0.9975-7
808            * src/{init.c,chm_common.c}, inst/include/*: export cholmod_analyze_p
809    
810    2006-11-30  Martin Maechler  <maechler@stat.math.ethz.ch>
811    
812            * R/diagMatrix.R (%*%): write a direct [diag o Csparse] method
813    
814    2006-11-29  Douglas Bates  <bates@stat.wisc.edu>
815    
816            * src/dgeMatrix.c (dgeMatrix_solve): Check error code from dgetri.
817            * tests/dg_Matrix.R: Add Barry Rowlingson's test of a matrix that
818            is exactly singular.
819    
820    2006-11-07  Martin Maechler  <maechler@stat.math.ethz.ch>
821    
822            * DESCRIPTION (Date): updated -> release 0.9975-6
823    
824    2006-11-06  Martin Maechler  <maechler@stat.math.ethz.ch>
825    
826            * R/Csparse.R (replCmat): symmetric indexing of symmetric matrix
827            now returns symmetric.
828    
829            * R/zzz.R ("diag<-"): replace "diag<-" in base for R <= 2.4.x
830    
831            * R/Matrix.R (.M.sub.i.2col):  new, for  M[ cbind(i,j) ] indexing.
832            * R/Matrix.R (.M.repl.i.2col): new, for  M[ cbind(i,j) ] <- value
833    
834            * R/Auxiliaries.R (.type.kind): added
835    
836    2006-11-04  Martin Maechler  <maechler@stat.math.ethz.ch>
837    
838            * src/cs.[ch]: updated to CSparse Version 2.0.3 by simply
839            running src/CSparse_install.sh
840    
841            * R/denseMatrix.R: "[": keep symmetric on symmetric indexing.
842    
843    2006-11-03  Martin Maechler  <maechler@stat.math.ethz.ch>
844    
845            * src/dsCMatrix.c (dsCMatrix_Csparse_solve): new
846            * R/dsCMatrix.R (solve): "fully-sparse" using the above.
847    
848            * R/AllClass.R: "pMatrix" now also inherits from "generalMatrix"
849    
850            * tests/Class+Meth.R (tstMatrixClass): now assure
851            the (important in method programming) property :
852    
853                    ###>>  Every "Matrix" is either
854                    ###>>  "general*", "symmetric*", "triangular*" or "diagonal*"
855    
856                    (where "*" stands for "Matrix")
857    
858            * R/Auxiliaries.R (diagU2N): now .Call()s Csparse_diagU2N for <Csparse>
859    
860            * R/dMatrix.R (Compare(<dMatrix>,<dMatrix>): update and
861            * tests/validObj.R: checks for "comparison"
862    
863            * R/sparseMatrix.R ([): improved indexing for sparse;
864                    trying to keep <symmetric>[ n, n] symmmetric
865    
866            * tests/indexing.R: indexing for logical sparse now ok
867    
868    
869    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
870    
871            * src/Tsparse.c: use xTsparse_validate() , and hence remove
872    
873            * src/{ltC,lsC,lgT}Matrix.[ch]: removed
874    
875    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
876    
877            * R/AllClass.R (Matrix-class): check length of dimnames in validity.
878    
879            * tests/simple.R: validObject() checking the above.
880    
881            * src/dgCMatrix.c (xCMatrix_validate): new, small and simple,
882            replacing both dgCMatrix_validate and lgCM*.
883    
884            * src/Csparse.c (Csparse_dense_prod, etc): do not lose dimnames;
885            fix dimnames setting in other places.
886            * src/chm_common.c (chm_dense_to_SEXP): now can pass dimnames
887    
888    2006-11-01  Martin Maechler  <maechler@stat.math.ethz.ch>
889    
890            * R/Csparse.R,src/Csparse.c, etc: tcrossprod(<CsparseM>,<CsparseM>)
891    
892            * R/sparseMatrix.R (isSymmetric): drop 'factors' slot for
893            symmetry test, via
894            * R/Auxiliaries.R (.as.dgC.0.factors):
895    
896    2006-11-01  Douglas Bates  <bates@r-project.org>
897    
898            * R/Csparse.R,src/Csparse.c,tests/matprod.R,
899            man/CsparseMatrix-class.Rd: crossprod(<CsparseMatrix>,
900            <CsparseMatrix>) added
901    
902    2006-10-30  Martin Maechler  <maechler@stat.math.ethz.ch>
903    
904            * tests/matprod.R: add a variation of Harri's example
905    
906            * R/dsparseMatrix.R: fix crossprod(<dsparse>, <dge>) to *not*
907            recursive infinitely.
908    
909            * R/dgCMatrix.R: + solve(<sparse>, <sparse>)
910    
911            * tests/indexing.R: add test for the "<" bug fixed 10-27 in R/dMatrix.R
912    
913    2006-10-28  Martin Maechler  <maechler@stat.math.ethz.ch>
914    
915            * tests/Class+Meth.R (tstMatrixClass): more: use non-trivial
916            matrix if possible; test m+m == 2*m; now test dgRMatrix.
917            * R/dgRMatrix.R (.to.dgR): a few more coercions, in order to
918            satisfy the above test.
919    
920    2006-10-27  Martin Maechler  <maechler@stat.math.ethz.ch>
921    
922            * R/Matrix.R (Ops):  <Matrix> o <matrix>  method added
923    
924            * R/dgCMatrix.R: solve(a, b="missing") based on
925            * src/dgCMatrix.c (dgCMatrix_matrix_solve): extend to work with
926            RHS = NULL.
927    
928            * R/diagMatrix.R (diagdiagprod): extend %*% etc to ldiMatrix;
929            add more (needed) [t]crossprod() methods.
930    
931            * man/ddiMatrix-class.Rd: more info, notably on 'diag'
932    
933            * R/Auxiliaries.R (as_CspClass): cleanup
934            (drop0): internal utility for "Csparse_drop(*, 0)"
935            (.bail.out.2): encourage active feedback
936    
937    2006-10-26  Martin Maechler  <maechler@stat.math.ethz.ch>
938    
939            * R/dMatrix.R(Compare): new(), then slots [no validity check]
940    
941            * src/Csparse.c (Csparse_validate): fixed (and more efficient in
942            non-valid or 'sorted' case).
943    
944            * R/dsparseMatrix.R: add "chol" method.
945            * R/ddenseMatrix.R: ditto
946    
947            * R/diagMatrix.R (Ops): group methods for  <diagonal> o <sparse>
948            * NAMESPACE (Ops)
949            * R/diagMatrix.R (diag2T): simple utility used "higher level"
950            coercion; deprecating direct lower level coercions.
951    
952            * R/*.R (seq): use seq_len() and seq_along() where possible.
953    
954    
955    2006-10-23  Martin Maechler  <maechler@stat.math.ethz.ch>
956    
957            * DESCRIPTION (Version): 0.9975-5 ready for release
958    
959    2006-10-20  Douglas Bates  <bates@stat.wisc.edu>
960    
961            * src/init.c (R_init_Matrix): export more cholmod CCallable functions.
962    
963    2006-10-20  Martin Maechler  <maechler@stat.math.ethz.ch>
964    
965            * R/AllClass.R (corMatrix): add 'validity' check;
966                    comment out unused "LDL" class definition
967            * NAMESPACE: mention, but do not export "LDL" class
968            * R/corMatrix.R: new (simple), needed for R-devel with
969            * tests/Class+Meth.R (tstMatrixClass): 1 exception for corMatrix
970              coerce and t() exceptions for all 5 'Mat.MatFact' classes.
971    
972    2006-10-19  Douglas Bates  <bates@stat.wisc.edu>
973    
974            * src/chm_common.h: Add R_cholmod_start to initialize cholmod to
975            use Rprintf and R's error handling.
976    
977    2006-10-17  Martin Maechler  <maechler@stat.math.ethz.ch>
978    
979            * R/diagMatrix.R (%*%): rep(*, each = .) in Matrix %*% diagonal.
980            * tests/matprod.R: add tests for the bug fixed.
981    
982    2006-10-11  Douglas Bates  <bates@stat.wisc.edu>
983    
984            * src/HBMM.[ch]: remove HarwellBoeing format for writing.
985            * src/SOURCES_C.mkf (SOURCES_C): no longer compile iohb.c
986    
987    2006-10-06  Douglas Bates  <bates@stat.wisc.edu>
988    
989            * R/d[gs]CMatrix.R: deprecate the writeHB function.  Use writeMM instead.
990    
991    2006-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
992    
993            * DESCRIPTION (Version): 0.9975-3
994    
995            * R/diagMatrix.R (bdiag): new function constructing block diagonal
996            (sparse) matrices.
997            * man/bdiag.Rd: docu + examples
998    
999            * R/Csparse.R (replCmat): calling new Csparse_drop() now.
1000    
1001            * src/Csparse.c (Csparse_general_to_symmetric, Csparse_drop): new functions
1002            * R/lsCMatrix.R: three more coercions to lsC (thanks to the above)
1003    
1004            * R/diagMatrix.R (Diagonal): '[<-' method for diag.matrices such
1005            that result is sparse or diagonal (and not dense).
1006    
1007            * man/Subassign-methods.Rd: fix examples
1008    
1009            * R/Matrix.R (Matrix):  Matrix(0, *) or Matrix(*, sparse=TRUE)
1010            should always return a sparse (and not sometimes a diagonal) matrix.
1011    
1012    2006-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
1013    
1014            * R/Matrix.R ([<-): also for value "Matrix" or "matrix"
1015    
1016    2006-10-04  Douglas Bates  <bates@stat.wisc.edu>
1017    
1018            * DESCRIPTION (Version): 0.9975-2
1019    
1020            * inst/include/Matrix_stubs.c (M_cholmod_sparse_to_triplet): export more symbols
1021    
1022    2006-10-02  Douglas Bates  <bates@R-project.org>
1023    
1024            * tests/dg_Matrix.R: Simplify test taking into account new code.
1025    
1026    2006-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
1027    
1028            * R/Csparse.R (replCmat): improve for missing i / j in non-simple cases
1029    
1030            * R/lsTMatrix.R: new files w/ missing methods
1031            * R/nsTMatrix.R:  "  'for completeness'
1032    
1033            * tests/Class+Meth.R: a bit less 'not.ok.classes'
1034    
1035            * R/Tsparse.R (t): generalized "t" method from "dgT*" to "Tsparse*"
1036    
1037    
1038    2006-09-28  Douglas Bates  <bates@R-project.org>
1039    
1040            * src/dppMatrix.h: Ensure definition of dspMatrix_validate is
1041            included.
1042    
1043            * src/init.c, inst/include/{Matrix.h,Matrix_stubs.h,cholmod.h}:
1044            Export C-callable functions used in Zt_create in lme4.
1045    
1046    2006-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
1047    
1048            * DESCRIPTION (Version): 0.9975-1
1049    
1050            * tests/simple.R: less checks fail; using NA, found that our
1051                    kronecker() is not base-compatible with NA's.
1052    
1053            * R/dMatrix.R: "Compare" method now implemented for all cases
1054    
1055            * R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility
1056    
1057            * man/dtpMatrix-class.Rd: mention length of 'x' slot
1058    
1059            * src/dtpMatrix.c (dtpMatrix_validate): fix check
1060            * src/dspMatrix.c (dspMatrix_validate): ditto
1061    
1062            * R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
1063              including coercion to [nl]tTMatrix.
1064    
1065            * R/diagMatrix.R (show): print a header line as for other classes.
1066    
1067    2006-09-27  Martin Maechler  <maechler@stat.math.ethz.ch>
1068    
1069            * src/Makefile.win (SUBDIRS): fix typo
1070    
1071    2006-09-19  Martin Maechler  <maechler@stat.math.ethz.ch>
1072    
1073            * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
1074    
1075    2006-09-18  Douglas Bates  <bates@stat.wisc.edu>
1076    
1077            * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
1078            symmetric and y missing in R code using %*% (cholmod_aat doesn't
1079            accept a symmetric matrix).
1080            * tests/group-methods.R: Uncomment test of crossprod applied to
1081            lsCMatrix objects.
1082    
1083    2006-09-18  Martin Maechler  <maechler@stat.math.ethz.ch>
1084    
1085            * R/AllClass.R (symmetricMatrix): add validity method (available
1086            in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
1087    
1088            * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
1089    
1090            * tests/indexing.Rout.save:
1091            * tests/indexing.R: additions, mainly for 'lsparse'
1092    
1093            * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
1094            case.
1095    
1096            * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
1097    
1098    2006-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
1099    
1100            * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
1101                    as 'N' (1-letter - Ok?)
1102    
1103            * tests/group-methods.R: add test for logical + NAs
1104    
1105            * R/dMatrix.R ("Compare"): fix to work with NA's
1106    
1107            * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
1108    
1109            * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
1110                    which is implemented.
1111    
1112    2006-09-15  Martin Maechler  <maechler@stat.math.ethz.ch>
1113    
1114            * src/chm_common.c: coerce logical <-> double instead of
1115            typecasting;  needed for "l" matrix handling in cholmod.
1116    
1117            * tests/other-pkgs.R (graph): small extension in "graph" checks.
1118    
1119            * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
1120            (Tsp2grNEL): other fixes needed
1121    
1122  2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
1123    
1124          * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"          * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
# Line 7  Line 1128 
1128          * tests/: adaptions          * tests/: adaptions
1129          * src/chm_common.c (chm_dense_to_SEXP): and others:          * src/chm_common.c (chm_dense_to_SEXP): and others:
1130                  new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL                  new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
1131          * src/Csparse.c, etc: dito          * src/Csparse.c, etc: ditto
1132    
1133  2006-09-11  Douglas Bates  <bates@R-project.org>  2006-09-11  Douglas Bates  <bates@R-project.org>
1134    
# Line 26  Line 1147 
1147          * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()          * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
1148    
1149          * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"          * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
1150          * man/tcrossprod.Rd: dito          * man/tcrossprod.Rd: ditto
1151    
1152  2006-09-08  Douglas Bates  <bates@stat.wisc.edu>  2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
1153    
# Line 69  Line 1190 
1190    
1191          * R/sparseMatrix.R (Arith): moved Arith group method one-level up          * R/sparseMatrix.R (Arith): moved Arith group method one-level up
1192          from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"          from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
1193          * R/dsparseMatrix.R: dito          * R/dsparseMatrix.R: ditto
1194          * R/Csparse.R: dito          * R/Csparse.R: ditto
1195    
1196  2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
1197    
# Line 86  Line 1207 
1207    
1208          * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's          * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
1209          * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.          * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
1210          (.is.diagonal): dito          (.is.diagonal): ditto
1211    
1212          * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's          * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
1213    

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