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revision 1548, Mon Sep 11 22:13:07 2006 UTC revision 2081, Sat Oct 6 22:01:45 2007 UTC
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1    2007-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * R/pMatrix.R: solve(<Matrix>, <pMatrix>)
4    
5    2007-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
6    
7            * R/LU.R: solve() method for "denseLU"
8    
9    2007-10-01  Martin Maechler  <maechler@stat.math.ethz.ch>
10    
11            * DESCRIPTION (Version): 0.999375-3 preparing for release
12    
13            * R/AllGeneric.R: simplify  if(.) .. else .. for R <= 2.5.1
14    
15            * R/Matrix.R (Matrix): .Internal(matrix(..)) different for R >= 2.7.0
16    
17    2007-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
18    
19            * R/pMatrix.R (.m.mult.pMat): fix <matrix> %*% <pMatrix>,
20              thanks to Kasper Kristensen.
21            * tests/matprod.R: regression test for that.
22    
23    2007-09-23 17:32  Douglas Bates <bates@stat.wisc.edu>
24    
25            * [r4778] R/AllGeneric.R: Check R version before defining generics for
26              primitives
27    
28    2007-09-13  Martin Maechler  <maechler@stat.math.ethz.ch>
29    
30            * R/denseMatrix.R (rcond): method
31            * R/sparseQR.R (rcond): method, use x or t(x)
32    
33    2007-09-12  Martin Maechler  <maechler@stat.math.ethz.ch>
34    
35            * R/dgeMatrix.R (rcond): method: work via qr.R() for non-square
36            matrices.
37            * R/sparseMatrix.R: Ditto for all other rcond() method definitions.
38    
39            * man/rcond.Rd: mention the more general definition, and add
40            example for non-square matrices.
41    
42            * man/chol.Rd: new file, for the S4 chol() generic and all methods.
43    
44    2007-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
45    
46            * R/sparseQR.R: add qr.R() method [to be used for rcond()]
47    
48    2007-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
49    
50            * R/Matrix.R ([<-): add (Matrix,missing,ANY,Matrix) etc
51            * tests/indexing.R: add new regression for the above cases.
52    
53    2007-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
54    
55            * src/Mutils.h (__sun): clause for alloca.h on Solaris
56    
57    2007-08-16  Martin Maechler  <maechler@stat.math.ethz.ch>
58    
59            * DESCRIPTION (Date, Version): 0.999375-2
60    
61    2007-08-15  Martin Maechler  <maechler@stat.math.ethz.ch>
62    
63            * R/HBMM.R (readMM): make work for pattern matrices as well
64    
65    2007-08-14 13:07  Douglas Bates <bates@stat.wisc.edu>
66    
67            * [r4730] src/Mutils.h: declare alloca
68            * [r4734] NAMESPACE, R/AllGeneric.R, R/Csparse.R, R/HBMM.R, R/Tsparse.R,
69              R/dgCMatrix.R, R/dgTMatrix.R, R/dsCMatrix.R, R/dsTMatrix.R,
70              man/externalFormats.Rd, src/Csparse.c, src/Csparse.h, src/DEPS.mkf,
71              src/HBMM.c, src/HBMM.h, src/Mutils.h, src/SOURCES_C.mkf, src/init.c,
72              src/mmio.c, src/mmio.h: Remove deprecated function writeHB and its
73              methods; switch writeMM to use CHOLMOD code; repair readMM
74    
75    2007-08-14  Martin Maechler  <maechler@stat.math.ethz.ch>
76    
77            * R/nearPD.R, man/nearPD.Rd (nearPD): new function built on Jens
78            Oehlschlaegel's ... result type still to be discussed!
79    
80    2007-08-10  Martin Maechler  <maechler@stat.math.ethz.ch>
81    
82            * man/image-methods.Rd: new, combining all image() methods
83    
84    2007-08-09  Martin Maechler  <maechler@stat.math.ethz.ch>
85    
86            * R/dgCMatrix.R: define qr() and lu() methods for "sparseMatrix"
87            to work via dgC...
88    
89            * R/Matrix.R (Matrix): special treatment for "table" (S3)
90    
91    2007-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
92    
93            * R/dgTMatrix.R (image): change defaults to
94                    aspect = "iso", colorkey = FALSE
95    
96    2007-08-06  Martin Maechler  <maechler@stat.math.ethz.ch>
97    
98            * src/dsyMatrix.c (dsyMatrix_matrix_mm): 'b' might be matrix;
99            must copy its *expanded* x slot before LAPACK call.
100    
101            * tests/matprod.R: test the last days' changes.
102    
103    2007-08-06 16:43  Douglas Bates <bates@stat.wisc.edu>
104    
105            * [r4712] inst/include/Matrix_stubs.c: Change R_cholmod_printf in stubs
106              as well as in sources
107            * [r4713] src/dsyMatrix.c: Duplicate the contents of the RHS before
108              Lapack call
109    
110    2007-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
111    
112            * R/Matrix.R (%*%, crossprod, tcrossprod): add method for
113                    ("Matrix", "matrix") which is needed in some cases.
114            Ditto for solve().
115    
116            * R/colSums.R (.as.dge.Fun): need ddenseMatrix methods to avoid
117            infinite recursion in dispatch for some cases.
118    
119    2007-08-02 08:48  Martin Maechler <maechler@stat.math.ethz.ch>
120    
121            * [r4693] src/chm_common.c: R_cholmod_printf() instead of Rprintf() just
122              so pointers match
123    
124    2007-08-02  Martin Maechler  <maechler@stat.math.ethz.ch>
125    
126            * DESCRIPTION (Date): set ready for release -- 0.999375-1
127    
128    2007-08-01 15:44  Douglas Bates <bates@stat.wisc.edu>
129    
130            * [r4686] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
131              src/chm_common.c, src/chm_common.h: Change API for
132              numeric_as_chm_dense and N_AS_CHM_DN
133    
134    2007-08-01  Martin Maechler  <maechler@stat.math.ethz.ch>
135    
136            * src/dtrMatrix.c (dtrMatrix_matrix_mm): fix dimensionality check (!)
137            * tests/matprod.R: regr.test for it
138    
139    2007-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
140    
141            * R/dMatrix.R: fix from Brian for   Math2(., digits = "missing")
142            * tests/group-methods.R: and regression-test it
143    
144    2007-07-19 19:45  Douglas Bates <bates@stat.wisc.edu>
145    
146            * [r4642] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
147              inst/include/cholmod.h, src/chm_common.c, src/init.c: Export
148              triplet_to_sparse, documentation, use typedefs
149    
150    2007-07-18  Martin Maechler  <maechler@stat.math.ethz.ch>
151    
152            * man/dpoMatrix-class.Rd: added 'corMatrix' example
153    
154            * src/dsyMatrix.[ch] (dsyMatrix_as_matrix): new 'keep_dimnames' arg
155            * src/dtrMatrix.[ch] (dtrMatrix_as_matrix): ditto
156            * src/init.c, R/dsyMatrix.R, R/dtrMatrix.R, R/lgTMatrix.R: ditto
157    
158            * R/lsparseMatrix.R: bug fix in "all" method
159            * R/Ops.R (.do.Logic.lsparse): "|" bug in borderline case
160    
161            * R/dsyMatrix.R (coerce->dsTMatrix): (i,j) slots should *not* have names
162            * R/ngTMatrix.R (coerce->ngTMatrix): ditto;
163                    + matrix |-> nMatrix coercion
164            * R/pMatrix.R: + setAs()  to dMatrix and from nMatrix
165            * man/pMatrix-class.Rd: ditto
166    
167            * R/Matrix.R (Summary): method for non-dMatrix
168    
169            * tests/Class+Meth.R (extraValid): new check about "dirty" slots
170            * tests/Class+Meth.R (tstMatrixClass): test norm(.);
171                    test all Summary methods.
172    
173    2007-07-16  Martin Maechler  <maechler@stat.math.ethz.ch>
174    
175            * R/dgeMatrix.R (norm, rcond): methods for 'matrix'
176    
177    2007-07-14  Martin Maechler  <maechler@stat.math.ethz.ch>
178    
179            * R/sparseMatrix.R (norm): simple methods for sparseMatrix
180    
181            * R/pMatrix.R (t?crossprod): methods for pMatrix
182    
183    2007-07-10  Douglas Bates  <bates@stat.wisc.edu>
184    
185            * src/dgeMatrix.c (dgeMatrix_colsums): Get the logic straight.
186    
187    2007-07-09 20:45  Douglas Bates <bates@stat.wisc.edu>
188    
189            * [r4579] src/dgeMatrix.c: Untangle horrible code in dgeMatrix_colsums
190              trying to fix a subtle bug - which has been somewhere else.
191    
192    2007-07-09 19:43  Martin Maechler <maechler@stat.math.ethz.ch>
193    
194            * [r4578] src/dgeMatrix.c: "cleaned" dgeMatrix_colsums() - but did not
195              solve the bug
196    
197    2007-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
198    
199            * src/dgCMatrix.c (compressed_to_TMatrix):
200    
201    2007-07-07  Martin Maechler  <maechler@stat.math.ethz.ch>
202    
203            * src/Csparse.c (Rsparse_validate): new, to have some validity
204            checking for RsparseMatrix
205            * src/dgCMatrix.c (xRMatrix_validate): ditto
206            * src/dtCMatrix.c (tRMatrix_validate): ditto
207    
208    2007-07-07  Douglas Bates <bates@stat.wisc.edu>
209    
210            * [r4567] R/AllClass.R: Slots already in RsparseMatrix were redefined in
211              lgRMatrix
212            * [r4568] DESCRIPTION: Prepare for bug-fix release
213            * [r4570] src/CHOLMOD/Check/cholmod_write.c: Include cholmod_matrixops.h
214              for declaration of cholmod_symmetry
215    
216    2007-07-06  Martin Maechler  <maechler@stat.math.ethz.ch>
217    
218            * DESCRIPTION (Version): 0.999375 merged into the trunk; ready for
219            release.
220    
221    2007-07-06 14:11  Douglas Bates <bates@stat.wisc.edu>
222    
223            * [r4559] src/iohb.c, src/iohb.h: Remove Harwell-Boeing input/output
224              functions - no longer used
225            * [r4560] src/HBMM.c, src/Mutils.c, src/dgTMatrix.c, src/dgeMatrix.c,
226              src/dspMatrix.c, src/dsyMatrix.c, src/dtCMatrix.c,
227              src/factorizations.c, src/sparseQR.c: Replace most calls to Calloc by
228              Alloca
229    
230    2007-07-06 13:14  Martin Maechler <maechler@stat.math.ethz.ch>
231    
232            * [r4558] inst/doc/Comparisons.Rnw, src/CHMfactor.c, src/Csparse.c,
233              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dense.c,
234              src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c, src/sparseQR.c,
235              src/t_gCMatrix_colSums.c: more R_CheckStack()s
236    
237    2007-07-05 18:12  Douglas Bates <bates@stat.wisc.edu>
238    
239            * [r4550] inst/include/Matrix.h: Add the macro N_AS_CHM_DN to "alloca"
240              the required amount of memory then call M_numeric_as_chm_dense.
241            * [r4556] src/Mutils.h, src/dgCMatrix.c: Define and use the Alloca macro
242              (like Calloc but calling alloca)
243    
244    2007-07-05  Martin Maechler  <maechler@stat.math.ethz.ch>
245    
246            * R/sparseMatrix.R (printSpMatrix): renamed from prSpMatrix()
247            and extended with more sophisticated 'col.names' option.
248            * NAMESPACE: export  printSparseMatrix()
249            * man/printSpMatrix.Rd: document, incl. examples
250    
251    2007-07-04 16:21  Douglas Bates <bates@stat.wisc.edu>
252    
253            * [r4543] src/cs_utils.c, src/cs_utils.h, src/dgCMatrix.c,
254              src/dtCMatrix.c, src/sparseQR.c: CSP typedef for *cs and macro
255              AS_CSP. API change - pass the empty structure to Matrix_as_cs.
256    
257    2007-07-04  Martin Maechler  <maechler@stat.math.ethz.ch>
258    
259            * DESCRIPTION (Version): 0.99875-4
260    
261            * tests/Class+Meth.R (tstMatrixClass): add dimnames, and hence test
262            some dimnames perservation.
263    
264            * R/dsTMatrix.R (t-method): keep dimnames
265            * R/dtTMatrix.R:  ditto
266    
267            * R/sparseMatrix.R (prSpMatrix): print colnames when non-trivial
268            and ncol(.) < 10
269    
270            * src/cs_utils.c: drop check_class() and use Matrix_check_class()
271            from Mutils.h
272    
273            * src/lgCMatrix.c ([ln]csc_to_matrix): no longer lose dimnames,
274            e.g. in as(<ngCMatrix>, "matrix")
275    
276    2007-07-01 13:27  Douglas Bates <bates@stat.wisc.edu>
277    
278            * [r4529] .: Create a branch for the API changes from the 0.99875
279              series to the 0.999375 series
280            * [r4530] DESCRIPTION, inst/include/Matrix.h,
281              inst/include/Matrix_stubs.c, src/CHMfactor.c, src/Csparse.c,
282              src/Mutils.h, src/Tsparse.c, src/chm_common.c, src/chm_common.h,
283              src/dense.c, src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c,
284              src/t_gCMatrix_colSums.c: API change - pass the empty structure to the
285              as_cholmod_x functions
286    
287    2007-06-30 09:05  Martin Maechler <maechler@stat.math.ethz.ch>
288    
289            * [r4527] trunk/Matrix/DESCRIPTION, trunk/Matrix/NAMESPACE,
290              trunk/Matrix/inst/doc/Comparisons.Rnw: add session- and hardware-info
291              to Comparisons
292    
293    >>>>>>> .merge-right.r4561
294    2007-06-29  Martin Maechler  <maechler@stat.math.ethz.ch>
295    
296            * DESCRIPTION (Version): 0.99875-3 ready to be released.
297    
298            * R/sparseMatrix.R (spMatrix): make spMatrix(3,4) working
299    
300            * R/AllGeneric.R: set "Math" (and "Math2") group generics in a way
301            that should also work in a future version of R.
302    
303    2007-06-21  Martin Maechler  <maechler@stat.math.ethz.ch>
304    
305            * NAMESPACE, R/AllClass.R: "xsparseVector" class union.
306    
307            * R/sparseVector.R: more *sparseVector coercions, notably for
308            non - double ones.
309    
310    2007-06-19  Martin Maechler  <maechler@stat.math.ethz.ch>
311    
312            * R/colSums.R: new file for all (col|row)(Sums|Means) methods,
313              notably the new ones building on the new .Call(.)s:
314    
315            * src/dgCMatrix.c (DEF_gCMatrix_COLSUMS): use to define
316            all 4 of [dlin]gCMatrix_colSums().
317    
318    2007-06-18 16:12  Douglas Bates <bates@stat.wisc.edu>
319    
320            * [r4472] src/Syms.h, src/init.c: Added Matrix_lengthSym
321            * [r4473] src/dgCMatrix.c: Modified dgCMatrix_colSums for sparseVector
322              result
323    
324    2007-06-16  Martin Maechler  <maechler@stat.math.ethz.ch>
325    
326            * R/kronecker.R: fix typo (could lead to inf.recursion)
327            * test/simple.R: testing that
328    
329            * R/sparseMatrix.R (prSpMatrix): change to be used as print()
330            method as well (which can have arguments, show() can't).
331    
332    2007-06-16 15:52  Douglas Bates <bates@stat.wisc.edu>
333    
334            * [r4466] R/dgCMatrix.R, src/dgCMatrix.c, src/dgCMatrix.h, src/init.c:
335              added dgCMatrix_colSums for [col,row][Sums,Means]
336    
337    2007-06-15 23:15  Douglas Bates <bates@stat.wisc.edu>
338    
339            * [r4460] R/sparseMatrix.R, man/dgCMatrix-class.Rd, src/dgCMatrix.c,
340              src/dgCMatrix.h, src/init.c: added lm.fit.sparse (unexported),
341              coercion of "factor" to "dgCMatrix" and dgCMatrix_cholsol
342            * [r4461] R/AllClass.R, man/sparseMatrix-class.Rd: draft "indicators"
343              class
344            * [r4463] R/sparseMatrix.R, man/dgCMatrix-class.Rd,
345              man/sparseMatrix-class.Rd: Don't need an "indicators" class - use the
346              row names to store the levels - duh!  Added an example.
347    
348    2007-06-14  Martin Maechler  <maechler@stat.math.ethz.ch>
349    
350            * src/Csparse.c (Csparse_validate): check for *repeated* entries
351            thanks to example from Christian Buchta; with a test here:
352            * tests/simple.R:
353    
354    2007-06-07  Martin Maechler  <maechler@stat.math.ethz.ch>
355    
356            * R/Auxiliaries.R (callGeneric): another fix, needed for some cases
357            of colSums(*, sparseResult = TRUE)
358    
359    2007-06-06  Martin Maechler  <maechler@stat.math.ethz.ch>
360    
361            * R/lsparseMatrix.R, R/ldenseMatrix.R (all, any): change default to
362            'na.rm = FALSE' as "everywhere" else in R.
363    
364    2007-06-05 Douglas Bates <bates@stat.wisc.edu>
365    
366            * [r4421] src/CSparse_install.sh: Modify for new organization of
367              CSparse package
368            * [r4425] src/UFsparse_download.sh: Update to version 3.0.0 of
369              SuiteSparse
370            * [r4426] src/Makefile: add ./UFconfig to the include path for
371              compilation
372            * [r4427] src/cs.[ch]: update to CSparse version 2.2.0
373            * [r4428] inst/doc/UFsparse/* src/{AMD,CHOLMOD,COLAMD}/*
374              src/UFconfig/UFconfig.h: Update to version 3.0.0 of SuiteSparse
375    
376    2007-06-05  Martin Maechler  <maechler@stat.math.ethz.ch>
377    
378            * R/Auxiliaries.R (emptyColnames): + argument msg.if.not.empty, used in
379            * R/sparseMatrix.R (prSpMatrix): now gives a message about
380            suppressed column names.
381    
382    2007-06-04 17:13  Douglas Bates <bates@stat.wisc.edu>
383    
384            * [r4418] src/Csparse.c, src/HBMM.c, src/Mutils.c, src/Mutils.h,
385              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dgCMatrix.c,
386              src/dgeMatrix.c, src/dpoMatrix.c, src/dpoMatrix.h, src/dppMatrix.c,
387              src/dppMatrix.h, src/dsCMatrix.c, src/dspMatrix.c, src/dspMatrix.h,
388              src/dsyMatrix.c, src/dsyMatrix.h, src/dtpMatrix.c, src/dtrMatrix.c:
389              Remove warnings after change to const char* CHAR
390    
391    2007-06-04 17:11  Douglas Bates <bates@stat.wisc.edu>
392    
393            * [r4417] inst/include/Matrix_stubs.c, inst/include/cholmod.h: Corrected
394              type of M_cholmod_ssmult
395    
396    2007-06-03 14:42  Douglas Bates <bates@stat.wisc.edu>
397    
398            * [r4412] inst/include/Matrix_stubs.c, inst/include/cholmod.h,
399              src/init.c: Yet another cholmod export - cholmod_ssmult
400    
401    2007-05-23  Martin Maechler  <maechler@stat.math.ethz.ch>
402    
403            * NAMESPACE: exported drop0(), since
404            * man/drop0.Rd: I have seen several cases, I really wanted to use
405            it, so our users may want too.
406    
407    2007-05-22  Martin Maechler  <maechler@stat.math.ethz.ch>
408    
409            * man/colSums.Rd: separately document colSums() etc, since these
410            have the extra argument 'sparseResult'.
411    
412    2007-05-21  Martin Maechler  <maechler@stat.math.ethz.ch>
413    
414            * R/sparseMatrix.R (spMatrix): utility (T)sparse Matrix constructor;
415            * man/spMatrix.Rd: docu., including examples
416    
417            * R/Auxiliaries.R (sp.colMeans): etc, using a patched callGeneric(),
418            in order to make colMeans() etc fast *and* correct.
419            * R/sparseVector.R (replSPvec): "[<-" functionality for
420            sparseVectors; tested in
421            * tests/simple.R:
422    
423    2007-05-19  Martin Maechler  <maechler@stat.math.ethz.ch>
424    
425            * R/sparseMatrix.R (print.sparseSummary): and summary() method for
426            (very) sparse Matrices; output similar to Matlab's print().
427    
428    2007-05-17  Douglas Bates  <bates@stat.wisc.edu>
429    
430            * src/HBMM.c (Matrix_writeMatrixMarket): Write 1-based, not
431            0-based, indices (Jose Quesada <quesada@gmail.com>).
432    
433    2007-05-16  Douglas Bates  <bates@stat.wisc.edu>
434    
435            * R/CHMfactor.R: Added solve methods for a CHMfactor object.
436    
437    2007-05-16  Martin Maechler  <maechler@stat.math.ethz.ch>
438    
439            * R/Auxiliaries.R (sparsapply): new utility, much faster than
440            tapply1() for large sparse matrices.
441    
442    2007-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
443    
444            * R/Matrix.R (dim<-): reshape now via sparseVector.
445    
446            * R/sparseVector.R: methods and function for
447            * R/AllClass.R: new "sparseVector" class and daughters.
448            * NAMESPACE: export new classes
449    
450    2007-05-14  Martin Maechler  <maechler@stat.math.ethz.ch>
451    
452            * DESCRIPTION (Version): 0.99875-1
453            * src/Makefile.win: also remove Lapack code from here (cf. 04-25).
454    
455    2007-05-11  Martin Maechler  <maechler@stat.math.ethz.ch>
456    
457            * R/Tsparse.R ([, Tsparse): fix last case: *duplicated*, symmetric
458            indexing
459            * tests/indexing.R: test set for that.
460    
461    2007-05-08  Martin Maechler  <maechler@stat.math.ethz.ch>
462    
463            * R/Tsparse.R (replTmat): fix the case of *duplicated* index
464            entries.
465            * tests/indexing.R(out): add regression test for it
466    
467    2007-04-30  Martin Maechler  <maechler@stat.math.ethz.ch>
468    
469            * R/(l(dense|sparse))?Matrix.R (!): use 'x', not 'e1' as argument
470            name for "!" method definitions.
471    
472    2007-04-26  Martin Maechler  <maechler@stat.math.ethz.ch>
473    
474            * R/Tsparse.R (intI): new utility, used for "[" :
475                    Cleanup up there, and fixes for duplicated indices - more TODO!
476    
477            * tests/indexing.R(out): more tests
478    
479    2007-04-25  Douglas Bates  <bates@stat.wisc.edu>
480    
481            * DESCRIPTION,src/Makefile: require R>= 2.5.0 and remove Lapack
482            code that is now part of the R Lapack library.
483    
484            * src/init.c,inst/include/{Matrix_stubs.c,cholmod.h}:export
485            cholmod_factorize_p (used in lme4 for GLMMs and NLMMs).
486    
487    2007-04-21  Martin Maechler  <maechler@stat.math.ethz.ch>
488    
489            * R/Matrix.R (image): method for all Matrices, not just sparse ones.
490    
491    2007-04-17  Martin Maechler  <maechler@stat.math.ethz.ch>
492    
493            * R/Auxiliaries.R (tapply1): unname(.) -> colSums() etc don't end
494            up with extraneous names '0'...'<n-1>'
495    
496    2007-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
497    
498            * R/dgTMatrix.R (mat2dgT): care about NAs
499    
500    2007-04-11  Martin Maechler  <maechler@stat.math.ethz.ch>
501    
502            * R/kronecker.R: triangularity preserving methods
503    
504    2007-03-27  Martin Maechler  <maechler@stat.math.ethz.ch>
505    
506            * R/kronecker.R: new file collecting kronecker() methods in one
507                    place.  Goal: become much faster!
508    
509    2007-03-23  Martin Maechler  <maechler@stat.math.ethz.ch>
510    
511            * src/dtCMatrix.c (dtCMatrix_solve): use the new code from Kasper
512            Kristensen based cs_spsolve() instead of _lsolve & _usolve which
513            can be much faster.
514    
515            * tests/matprod.R: add regression tests for these (upper & lower).
516    
517    2007-03-19  Martin Maechler  <maechler@stat.math.ethz.ch>
518    
519            * R/Matrix.R (diff): method for our Matrices.
520    
521            * R/sparseMatrix.R (isDiagonal): check dim()!
522    
523    2007-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
524    
525            * R/Matrix.R (dim<-): new method for "reshape()" built on a
526            proposal from Tamas Papp.
527    
528    2007-03-16  Martin Maechler  <maechler@stat.math.ethz.ch>
529    
530            * R/AllGeneric.R: remove all  if(!isGeneric(.))  clauses
531    
532            * R/zzz.R (.onLoad, .onUnload): do *not* leave bind_activation(TRUE);
533            rather define and export  cBind() and rBind() only.
534            --> useRs *must* change code that used to have cbind()/rbind() !!
535    
536            * R/bind.R: change tests from cbind() to cBind() and similarly to rBind()
537            * R/bind.Rout.save: ditto
538    
539    2007-02-16  Douglas Bates  <bates@r-project.org>
540    
541            * DESCRIPTION (Date, Version): 0.9975-11 with new date
542            * src/dgCMatrix.c (R_to_CMatrix, compressed_to_TMatrix): remove
543            const modifier on declaration of the array 'valid'
544    
545    2007-02-12  Douglas Bates  <bates@stat.wisc.edu>
546    
547            * R/CHMfactor.R: Add image method (coercion to sparseMatrix).
548    
549    2007-02-05  Martin Maechler  <maechler@stat.math.ethz.ch>
550    
551            * DESCRIPTION (Date, Version): 0.9975-10 with new date.
552    
553            * R/Ops.R (Arith): make sure Csparse o Csparse also works for e.g. ntCMatrix
554            * tests/simple.R: test the above and some of these coercions:
555    
556            * R/nsparseMatrix.R: coercing "Csparse" to "lsparseMatrix";
557                    be careful to avoid infinite recursion, using new coercions in
558            * R/ngCMatrix.R and nsC... and ntC...
559            * R/lsparseMatrix.R: ditto
560    
561            * R/SparseM-conv.R: more conversion, notably for triplet matrices.
562    
563            * src/dgCMatrix.c (R_to_C_Matrix): port Doug's fix and
564            * R/Rsparse.R: reactivate .Call()s
565    
566            * tests/Class+Meth.R: a bit more on actual classes
567    
568    2007-02-04  Douglas Bates  <bates@stat.wisc.edu>
569    
570            * src/dgCMatrix.c (compressed_to_TMatrix): fix memory bug using strdup()
571    
572    2007-02-03  Martin Maechler  <maechler@stat.math.ethz.ch>
573    
574            * DESCRIPTION (Version): 0.9975-10 to upload
575    
576            * tests/Class+Meth.R (tstMatrixClass): require coercions to
577            specific classes less unconditionally.
578    
579            * R/Auxiliaries.R: get rid of as_Tsparse() and as_Rsparse()
580    
581            * R/Tsparse.R (triu): etc, use as(*, "TsparseMatrix") instead of as_Tsparse()
582    
583            * R/Rsparse.R (.R.2.T): R-level workaround using compressed_to_TMatrix.
584            * R/Rsparse.R (.R.2.C): R-level workaround since C-level
585            R_to_CMatrix segfaults on one platform.
586            Eliminate most coercion method to *specific* classes, and replace
587            with virtual classes coercions.
588    
589    
590    2007-02-01  Martin Maechler <maechler@stat.math.ethz.ch>
591    
592            * src/init.c: export the CHM...._validate() placeholders, since
593            they *are* called.
594    
595            * tests/Class+Meth.R (classCanCoerce): and starting to test
596            all as(<from>, <to>)
597    
598    2007-01-30  Martin Maechler  <maechler@stat.math.ethz.ch>
599    
600            * R/Tsparse.R ([): more care when subsetting triangular Tsparse
601            * tests/indexing.R: tested now
602            * tests/indexing.Rout.save: updated
603    
604            * src/Csparse.c (Csparse_to_dense): use Rkind = -1 for PATTERN to
605            * src/chm_common.c (chm_dense_to_SEXP): return "ngeMatrix" when
606            appropriate.
607    
608            * NAMESPACE: export a trivial
609            * R/Matrix.R: drop() Matrix-method
610    
611            * R/AllClass.R: moved all prototypes to virtual super classes.
612    
613            * R/Rsparse.R: many more coercions to have less exceptions in
614            * tests/Class+Meth.R:
615    
616            * R/Ops.R (Compare): tweak for case with NA
617            * tests/simpl.R: hence another 'FIXME' eliminated
618    
619    2007-01-29  Martin Maechler  <maechler@stat.math.ethz.ch>
620    
621            * R/diagMatrix.R (solve): the obvious methods for diagonalMatrix
622            objects.
623    
624            * tests/Class+Meth.R (tstMatrixClass): now testing diag(), nnzero(),
625              and more of "!", "&", "|", all, any; coercions
626    
627            * R/Rsparse.R: many coercions (which enable quite a few other
628            methods), thanks to enhancements in
629            * src/dgCMatrix.c (R_to_CMatrix): new, and
630            * src/dgCMatrix.c (compressed_to_TMatrix): now for (d,l,n) ,
631            symmetric & triangular and ..RMatrix objects.
632    
633            * src/TMatrix_as.c (Matrix_T_as_DENSE,Matrix_T_as_GENERAL):
634            renamed file from src/dsTMatrix.c;
635            now dealing with symmetric and triangular Tsparse coercions, both
636            to dense and general.
637    
638    2007-01-27  Martin Maechler  <maechler@stat.math.ethz.ch>
639    
640            * src/dsTMatrix.c: has now "l" and "n" methods besides the "d" ones.
641    
642            * R/Ops.R (Arith): <dgCMatrix> o <numeric> now remains sparse
643            where sensible when the <numeric> is of length > 1.
644    
645    2007-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
646    
647            * R/Matrix.R ([<-): for M[] <- value: fix length
648    
649    2007-01-25  Martin Maechler  <maechler@stat.math.ethz.ch>
650    
651            * R/Auxiliaries.R (n2l_Matrix): new, to be used in
652            * R/ndenseMatrix.R: new coercions n* -> l*
653    
654    2007-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
655    
656            * R/triangularMatrix.R: new file; simple triu() and tril() methods.
657    
658            * R/Ops.R ("Logic"): and other "Ops", many updates
659    
660    2007-01-18  Martin Maechler  <maechler@stat.math.ethz.ch>
661    
662            * src/Mutils.h (SET_DimNames): new utility
663    
664            * R/Auxiliaries.R (nnzero): improved and now exported via
665    
666            * NAMESPACE: + nnzero(); length() == prod(dim(.)) method for all "Matrix" objects
667    
668    2007-01-17  Martin Maechler  <maechler@stat.math.ethz.ch>
669    
670            * R/diagMatrix.R (!): fix typo.
671    
672    2007-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
673    
674            * R/Auxiliaries.R (as_Csparse): and quite a few others:
675                    allow to pass class definition --> speedup
676            * R/sparseMatrix.R: apply the above
677    
678            * R/Csparse.R: coercion Csparse* to dense* now preserves shape properties.
679    
680            * src/Mutils.h (mMatrix_as_geMatrix): new, based on
681            * src/Mutils.c (dup_mMatrix_as_geMatrix): new; generalization of
682            old dup_mMatrix_as_dgeMatrix), eliminating a long-standing "FIXME".
683    
684            * src/dense.c (dense_to_Csparse): use new mMatrix_as_geMatrix()
685    
686            * R/denseMatrix.R (.dense2C): based on dense_to_Csparse: name it,
687            and use it for "sparse*" as well, since it's faster than the
688            as_Csparse(.) way.
689    
690    2007-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
691    
692            * R/Ops.R ("Logic"): more methods, notably an  <lgC> o <lgC> one.
693    
694    2007-01-12  Martin Maechler  <maechler@stat.math.ethz.ch>
695    
696            * R/Tsparse.R (.TM.repl.i.2col): new internal function to be used
697            as method for   M[ ij ] <- v
698            * R/Csparse.R:: go via Tsparse for "M[ij] <- v"
699    
700            * R/Ops.R: "Compare" for (C|R)sparse: need pointer slot for all
701            FALSE answer
702    
703            * R/Csparse.R (replCmat): fix the "all non-zero" case with reordering
704            * tests/indexing.R: test it, and some of the above
705    
706    2007-01-05  Martin Maechler  <maechler@stat.math.ethz.ch>
707    
708            * R/Auxiliaries.R (is_duplicatedT): new utility
709    
710    2007-01-05  Douglas Bates  <bates@stat.wisc.edu>
711    
712            * src/init.c (R_init_Matrix): export cholmod_scale
713    
714    2006-12-30  Martin Maechler  <maechler@stat.math.ethz.ch>
715    
716            * R/zzz.R (tmp): for R >= 2.5.0, extend formals of our
717            base::as.matrix to (x, ...)
718    
719    2006-12-28  Martin Maechler  <maechler@stat.math.ethz.ch>
720    
721            * R/Ops.R ("Arith" etc): move almost all "Ops" methods to new R
722            file; start using "Logic", hence
723    
724            * DESCRIPTION (Depends): R >= 2.4.1 (since we want "Logic")
725            * NAMESPACE: import and export "Logic"
726    
727    2006-12-27  Martin Maechler  <maechler@stat.math.ethz.ch>
728    
729            * src/zpotfr.f and dependencies: use LAPACK 3.1 version
730            only needed previously to R version 2.5.0.
731    
732    2006-12-26  Martin Maechler  <maechler@stat.math.ethz.ch>
733    
734            * DESCRIPTION (Date, Version): 0.9975-8, ready for release
735    
736            * R/Tsparse.R (replTmat): fix subassignment of triangular
737            * R/Csparse.R (replCmat): ditto
738            * tests/indexing.R: more tests, incl the above fix
739    
740    2006-12-23  Martin Maechler  <maechler@stat.math.ethz.ch>
741    
742            * R/Auxiliaries.R (drop0): extend for non CSparse
743            * R/Auxiliaries.R (diagU2N): should work for all sparseMatrix
744    
745            * src/Csparse.c (Csparse_to_Tsparse, Csparse_general_to_symmetric):
746                    use uplo correctly (!); other places: use uplo_P() macro
747    
748            * R/Csparse.R (replCmat): call diagU2N() when needed
749            * R/Tsparse.R (replTmat): ditto
750    
751            * src/dtCMatrix.c (tCMatrix_validate): new
752            * src/dtTMatrix.c (tTMatrix_validate): new, used in
753            * R/AllClass.R: for validity of dtC, dsC, and dtT, dsT.
754    
755            * R/diagMatrix.R (replDiag): to use in [<-
756    
757    2006-12-22  Martin Maechler  <maechler@stat.math.ethz.ch>
758    
759            * R/Auxiliaries.R (as_Csparse2, as_geSimpl): new functions;
760                    also more general diagU2N().
761    
762    2006-12-21  Martin Maechler  <maechler@stat.math.ethz.ch>
763    
764            * R/bind2.R: new file for all cbind2(), rbind() methods moved here
765            from R/<foo>Matrix.R files. Better diagonal & improved sparse methods.
766    
767    2006-12-20  Martin Maechler  <maechler@stat.math.ethz.ch>
768    
769            * tests/bind.R: a few more cases
770            * R/Auxiliaries.R (.M.kind): also work for atomic vectors
771    
772            * R/denseMatrix.R (cbind2/rbind2): moved here (and generalized) from
773            * R/ddenseMatrix.R (cbind2/rbind2)
774            * R/Tsparse.R (replTmat): final(?!) fix for "[<-" ..
775            * tests/indexing.R
776            * tests/indexing.Rout.save: updated
777    
778    2006-12-18  Martin Maechler  <maechler@stat.math.ethz.ch>
779    
780            * R/Tsparse.R (replTmat): fixed a remaining "[<-" bug in
781            * tests/indexing.R
782    
783    2006-12-15  Martin Maechler  <maechler@stat.math.ethz.ch>
784    
785            * R/sparseMatrix.R (prSpMatrix): "." alignment much improved:
786            align with proper position of "0", i.e., right for integers.
787            argument 'align' by default is "fancy".
788    
789    2006-12-14  Martin Maechler  <maechler@stat.math.ethz.ch>
790    
791            * R/sparseMatrix.R: delegate "Compare" to "Csparse.."
792            * R/Csparse.R: and fix "Compare" for more cases.
793            * tests/Class+Meth.R: test some of these (m == m, m != m)
794    
795    2006-12-13  Martin Maechler  <maechler@stat.math.ethz.ch>
796    
797            * R/lsparseMatrix.R: all() and any() methods
798            * R/ldenseMatrix.R:      ditto
799            * NAMESPACE, R/Matrix.R: ditto
800    
801            * man/all-methods.Rd: document them minimally
802    
803            * tests/simple.R: add a few examples for these
804    
805    2006-12-11  Martin Maechler  <maechler@stat.math.ethz.ch>
806    
807            * R/Tsparse.R ([): fix long standing typo in symmetric case
808            * man/dsCMatrix-class.Rd: add example exhibiting the above case
809    
810    2006-12-10  Douglas Bates  <bates@stat.wisc.edu>
811    
812            * src/CHMfactor.c (CHMfactor_to_sparse): change LDL factorization
813            to LL before converting to a sparse matrix. (The LDL form can be
814            converted to a sparse matrix but it is implicitly a unit
815            triangular matrix and a diagonal matrix overwritten on the diagonal.)
816    
817    2006-12-09  Douglas Bates  <bates@stat.wisc.edu>
818    
819            * src/chm_common.c (chm_factor_to_SEXP): allocate and fill the Dim slot.
820    
821    2006-12-08  Douglas Bates  <bates@stat.wisc.edu>
822    
823            * DESCRIPTION (Version): updated -> release 0.9975-7
824            * src/{init.c,chm_common.c}, inst/include/*: export cholmod_analyze_p
825    
826    2006-11-30  Martin Maechler  <maechler@stat.math.ethz.ch>
827    
828            * R/diagMatrix.R (%*%): write a direct [diag o Csparse] method
829    
830    2006-11-29  Douglas Bates  <bates@stat.wisc.edu>
831    
832            * src/dgeMatrix.c (dgeMatrix_solve): Check error code from dgetri.
833            * tests/dg_Matrix.R: Add Barry Rowlingson's test of a matrix that
834            is exactly singular.
835    
836    2006-11-07  Martin Maechler  <maechler@stat.math.ethz.ch>
837    
838            * DESCRIPTION (Date): updated -> release 0.9975-6
839    
840    2006-11-06  Martin Maechler  <maechler@stat.math.ethz.ch>
841    
842            * R/Csparse.R (replCmat): symmetric indexing of symmetric matrix
843            now returns symmetric.
844    
845            * R/zzz.R ("diag<-"): replace "diag<-" in base for R <= 2.4.x
846    
847            * R/Matrix.R (.M.sub.i.2col):  new, for  M[ cbind(i,j) ] indexing.
848            * R/Matrix.R (.M.repl.i.2col): new, for  M[ cbind(i,j) ] <- value
849    
850            * R/Auxiliaries.R (.type.kind): added
851    
852    2006-11-04  Martin Maechler  <maechler@stat.math.ethz.ch>
853    
854            * src/cs.[ch]: updated to CSparse Version 2.0.3 by simply
855            running src/CSparse_install.sh
856    
857            * R/denseMatrix.R: "[": keep symmetric on symmetric indexing.
858    
859    2006-11-03  Martin Maechler  <maechler@stat.math.ethz.ch>
860    
861            * src/dsCMatrix.c (dsCMatrix_Csparse_solve): new
862            * R/dsCMatrix.R (solve): "fully-sparse" using the above.
863    
864            * R/AllClass.R: "pMatrix" now also inherits from "generalMatrix"
865    
866            * tests/Class+Meth.R (tstMatrixClass): now assure
867            the (important in method programming) property :
868    
869                    ###>>  Every "Matrix" is either
870                    ###>>  "general*", "symmetric*", "triangular*" or "diagonal*"
871    
872                    (where "*" stands for "Matrix")
873    
874            * R/Auxiliaries.R (diagU2N): now .Call()s Csparse_diagU2N for <Csparse>
875    
876            * R/dMatrix.R (Compare(<dMatrix>,<dMatrix>): update and
877            * tests/validObj.R: checks for "comparison"
878    
879            * R/sparseMatrix.R ([): improved indexing for sparse;
880                    trying to keep <symmetric>[ n, n] symmmetric
881    
882            * tests/indexing.R: indexing for logical sparse now ok
883    
884    
885    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
886    
887            * src/Tsparse.c: use xTsparse_validate() , and hence remove
888    
889            * src/{ltC,lsC,lgT}Matrix.[ch]: removed
890    
891    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
892    
893            * R/AllClass.R (Matrix-class): check length of dimnames in validity.
894    
895            * tests/simple.R: validObject() checking the above.
896    
897            * src/dgCMatrix.c (xCMatrix_validate): new, small and simple,
898            replacing both dgCMatrix_validate and lgCM*.
899    
900            * src/Csparse.c (Csparse_dense_prod, etc): do not lose dimnames;
901            fix dimnames setting in other places.
902            * src/chm_common.c (chm_dense_to_SEXP): now can pass dimnames
903    
904    2006-11-01  Martin Maechler  <maechler@stat.math.ethz.ch>
905    
906            * R/Csparse.R,src/Csparse.c, etc: tcrossprod(<CsparseM>,<CsparseM>)
907    
908            * R/sparseMatrix.R (isSymmetric): drop 'factors' slot for
909            symmetry test, via
910            * R/Auxiliaries.R (.as.dgC.0.factors):
911    
912    2006-11-01  Douglas Bates  <bates@r-project.org>
913    
914            * R/Csparse.R,src/Csparse.c,tests/matprod.R,
915            man/CsparseMatrix-class.Rd: crossprod(<CsparseMatrix>,
916            <CsparseMatrix>) added
917    
918    2006-10-30  Martin Maechler  <maechler@stat.math.ethz.ch>
919    
920            * tests/matprod.R: add a variation of Harri's example
921    
922            * R/dsparseMatrix.R: fix crossprod(<dsparse>, <dge>) to *not*
923            recursive infinitely.
924    
925            * R/dgCMatrix.R: + solve(<sparse>, <sparse>)
926    
927            * tests/indexing.R: add test for the "<" bug fixed 10-27 in R/dMatrix.R
928    
929    2006-10-28  Martin Maechler  <maechler@stat.math.ethz.ch>
930    
931            * tests/Class+Meth.R (tstMatrixClass): more: use non-trivial
932            matrix if possible; test m+m == 2*m; now test dgRMatrix.
933            * R/dgRMatrix.R (.to.dgR): a few more coercions, in order to
934            satisfy the above test.
935    
936    2006-10-27  Martin Maechler  <maechler@stat.math.ethz.ch>
937    
938            * R/Matrix.R (Ops):  <Matrix> o <matrix>  method added
939    
940            * R/dgCMatrix.R: solve(a, b="missing") based on
941            * src/dgCMatrix.c (dgCMatrix_matrix_solve): extend to work with
942            RHS = NULL.
943    
944            * R/diagMatrix.R (diagdiagprod): extend %*% etc to ldiMatrix;
945            add more (needed) [t]crossprod() methods.
946    
947            * man/ddiMatrix-class.Rd: more info, notably on 'diag'
948    
949            * R/Auxiliaries.R (as_CspClass): cleanup
950            (drop0): internal utility for "Csparse_drop(*, 0)"
951            (.bail.out.2): encourage active feedback
952    
953    2006-10-26  Martin Maechler  <maechler@stat.math.ethz.ch>
954    
955            * R/dMatrix.R(Compare): new(), then slots [no validity check]
956    
957            * src/Csparse.c (Csparse_validate): fixed (and more efficient in
958            non-valid or 'sorted' case).
959    
960            * R/dsparseMatrix.R: add "chol" method.
961            * R/ddenseMatrix.R: ditto
962    
963            * R/diagMatrix.R (Ops): group methods for  <diagonal> o <sparse>
964            * NAMESPACE (Ops)
965            * R/diagMatrix.R (diag2T): simple utility used "higher level"
966            coercion; deprecating direct lower level coercions.
967    
968            * R/*.R (seq): use seq_len() and seq_along() where possible.
969    
970    
971    2006-10-23  Martin Maechler  <maechler@stat.math.ethz.ch>
972    
973            * DESCRIPTION (Version): 0.9975-5 ready for release
974    
975    2006-10-20  Douglas Bates  <bates@stat.wisc.edu>
976    
977            * src/init.c (R_init_Matrix): export more cholmod CCallable functions.
978    
979    2006-10-20  Martin Maechler  <maechler@stat.math.ethz.ch>
980    
981            * R/AllClass.R (corMatrix): add 'validity' check;
982                    comment out unused "LDL" class definition
983            * NAMESPACE: mention, but do not export "LDL" class
984            * R/corMatrix.R: new (simple), needed for R-devel with
985            * tests/Class+Meth.R (tstMatrixClass): 1 exception for corMatrix
986              coerce and t() exceptions for all 5 'Mat.MatFact' classes.
987    
988    2006-10-19  Douglas Bates  <bates@stat.wisc.edu>
989    
990            * src/chm_common.h: Add R_cholmod_start to initialize cholmod to
991            use Rprintf and R's error handling.
992    
993    2006-10-17  Martin Maechler  <maechler@stat.math.ethz.ch>
994    
995            * R/diagMatrix.R (%*%): rep(*, each = .) in Matrix %*% diagonal.
996            * tests/matprod.R: add tests for the bug fixed.
997    
998    2006-10-11  Douglas Bates  <bates@stat.wisc.edu>
999    
1000            * src/HBMM.[ch]: remove HarwellBoeing format for writing.
1001            * src/SOURCES_C.mkf (SOURCES_C): no longer compile iohb.c
1002    
1003    2006-10-06  Douglas Bates  <bates@stat.wisc.edu>
1004    
1005            * R/d[gs]CMatrix.R: deprecate the writeHB function.  Use writeMM instead.
1006    
1007    2006-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
1008    
1009            * DESCRIPTION (Version): 0.9975-3
1010    
1011            * R/diagMatrix.R (bdiag): new function constructing block diagonal
1012            (sparse) matrices.
1013            * man/bdiag.Rd: docu + examples
1014    
1015            * R/Csparse.R (replCmat): calling new Csparse_drop() now.
1016    
1017            * src/Csparse.c (Csparse_general_to_symmetric, Csparse_drop): new functions
1018            * R/lsCMatrix.R: three more coercions to lsC (thanks to the above)
1019    
1020            * R/diagMatrix.R (Diagonal): '[<-' method for diag.matrices such
1021            that result is sparse or diagonal (and not dense).
1022    
1023            * man/Subassign-methods.Rd: fix examples
1024    
1025            * R/Matrix.R (Matrix):  Matrix(0, *) or Matrix(*, sparse=TRUE)
1026            should always return a sparse (and not sometimes a diagonal) matrix.
1027    
1028    2006-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
1029    
1030            * R/Matrix.R ([<-): also for value "Matrix" or "matrix"
1031    
1032    2006-10-04  Douglas Bates  <bates@stat.wisc.edu>
1033    
1034            * DESCRIPTION (Version): 0.9975-2
1035    
1036            * inst/include/Matrix_stubs.c (M_cholmod_sparse_to_triplet): export more symbols
1037    
1038    2006-10-02  Douglas Bates  <bates@R-project.org>
1039    
1040            * tests/dg_Matrix.R: Simplify test taking into account new code.
1041    
1042    2006-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
1043    
1044            * R/Csparse.R (replCmat): improve for missing i / j in non-simple cases
1045    
1046            * R/lsTMatrix.R: new files w/ missing methods
1047            * R/nsTMatrix.R:  "  'for completeness'
1048    
1049            * tests/Class+Meth.R: a bit less 'not.ok.classes'
1050    
1051            * R/Tsparse.R (t): generalized "t" method from "dgT*" to "Tsparse*"
1052    
1053    
1054    2006-09-28  Douglas Bates  <bates@R-project.org>
1055    
1056            * src/dppMatrix.h: Ensure definition of dspMatrix_validate is
1057            included.
1058    
1059            * src/init.c, inst/include/{Matrix.h,Matrix_stubs.h,cholmod.h}:
1060            Export C-callable functions used in Zt_create in lme4.
1061    
1062    2006-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
1063    
1064            * DESCRIPTION (Version): 0.9975-1
1065    
1066            * tests/simple.R: less checks fail; using NA, found that our
1067                    kronecker() is not base-compatible with NA's.
1068    
1069            * R/dMatrix.R: "Compare" method now implemented for all cases
1070    
1071            * R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility
1072    
1073            * man/dtpMatrix-class.Rd: mention length of 'x' slot
1074    
1075            * src/dtpMatrix.c (dtpMatrix_validate): fix check
1076            * src/dspMatrix.c (dspMatrix_validate): ditto
1077    
1078            * R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
1079              including coercion to [nl]tTMatrix.
1080    
1081            * R/diagMatrix.R (show): print a header line as for other classes.
1082    
1083    2006-09-27  Martin Maechler  <maechler@stat.math.ethz.ch>
1084    
1085            * src/Makefile.win (SUBDIRS): fix typo
1086    
1087    2006-09-19  Martin Maechler  <maechler@stat.math.ethz.ch>
1088    
1089            * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
1090    
1091    2006-09-18  Douglas Bates  <bates@stat.wisc.edu>
1092    
1093            * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
1094            symmetric and y missing in R code using %*% (cholmod_aat doesn't
1095            accept a symmetric matrix).
1096            * tests/group-methods.R: Uncomment test of crossprod applied to
1097            lsCMatrix objects.
1098    
1099    2006-09-18  Martin Maechler  <maechler@stat.math.ethz.ch>
1100    
1101            * R/AllClass.R (symmetricMatrix): add validity method (available
1102            in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
1103    
1104            * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
1105    
1106            * tests/indexing.Rout.save:
1107            * tests/indexing.R: additions, mainly for 'lsparse'
1108    
1109            * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
1110            case.
1111    
1112            * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
1113    
1114    2006-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
1115    
1116            * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
1117                    as 'N' (1-letter - Ok?)
1118    
1119            * tests/group-methods.R: add test for logical + NAs
1120    
1121            * R/dMatrix.R ("Compare"): fix to work with NA's
1122    
1123            * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
1124    
1125            * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
1126                    which is implemented.
1127    
1128    2006-09-15  Martin Maechler  <maechler@stat.math.ethz.ch>
1129    
1130            * src/chm_common.c: coerce logical <-> double instead of
1131            typecasting;  needed for "l" matrix handling in cholmod.
1132    
1133            * tests/other-pkgs.R (graph): small extension in "graph" checks.
1134    
1135            * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
1136            (Tsp2grNEL): other fixes needed
1137    
1138  2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
1139    
1140          * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"          * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
# Line 7  Line 1144 
1144          * tests/: adaptions          * tests/: adaptions
1145          * src/chm_common.c (chm_dense_to_SEXP): and others:          * src/chm_common.c (chm_dense_to_SEXP): and others:
1146                  new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL                  new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
1147          * src/Csparse.c, etc: dito          * src/Csparse.c, etc: ditto
1148    
1149  2006-09-11  Douglas Bates  <bates@R-project.org>  2006-09-11  Douglas Bates  <bates@R-project.org>
1150    
# Line 26  Line 1163 
1163          * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()          * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
1164    
1165          * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"          * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
1166          * man/tcrossprod.Rd: dito          * man/tcrossprod.Rd: ditto
1167    
1168  2006-09-08  Douglas Bates  <bates@stat.wisc.edu>  2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
1169    
# Line 69  Line 1206 
1206    
1207          * R/sparseMatrix.R (Arith): moved Arith group method one-level up          * R/sparseMatrix.R (Arith): moved Arith group method one-level up
1208          from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"          from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
1209          * R/dsparseMatrix.R: dito          * R/dsparseMatrix.R: ditto
1210          * R/Csparse.R: dito          * R/Csparse.R: ditto
1211    
1212  2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
1213    
# Line 86  Line 1223 
1223    
1224          * 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
1225          * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.          * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
1226          (.is.diagonal): dito          (.is.diagonal): ditto
1227    
1228          * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's          * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
1229    

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