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revision 1716, Sat Jan 6 02:01:24 2007 UTC revision 2102, Fri Jan 11 22:35:25 2008 UTC
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1    2008-01-11  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * DESCRIPTION (Date): make ready for release
4    
5            * R/dgeMatrix.R: fix rcond() method for "dgeMatrix".
6    
7    2007-12-08  Martin Maechler  <maechler@stat.math.ethz.ch>
8    
9            * R/pMatrix.R: as(*, "matrix") now returns 0/1 *integer* matrix,
10                    and hence does as.vector(.).
11            * man/pMatrix-class.Rd: docs
12            * R/sparseMatrix.R: fix for printing "integer sparse"
13    
14            * tests/Class+Meth.R (tstMatrixClass): test M[FALSE], M[2] etc
15    
16            * R/Matrix.R and others: use "exact" function argument list for
17                    both "["   : (x, i,j, ..., drop)
18                    and  "[<-" : (x, i,j, ..., value)
19    
20            * R/denseMatrix.R: M[i] and M[i] <- v  (i vector) now work
21            * R/Tsparse.R (replTmat):    ditto
22            * R/diagMatrix.R (replDiag): ditto
23            * R/Csparse.R (replCmat):    ditto {was it worth the pain?}
24            * tests/indexing.R: testing the above
25    
26    2007-12-07  Martin Maechler  <maechler@stat.math.ethz.ch>
27    
28            * R/sparseMatrix.R (cov2cor): method for sparse matrices
29    
30            * R/diagMatrix.R ([<-): fix   D[ cbind(i,j) ] <- v
31    
32            * R/bind2.R: fix for Rsparse* and rbind2(dense,dense)
33    
34            * tests/Class+Meth.R: test cbind2, rbind2  and  diag<-
35    
36    2007-12-06  Martin Maechler  <maechler@stat.math.ethz.ch>
37    
38            * R/Matrix.R: "generic" cov2cor() method
39    
40            * R/nearPD.R: new 'only.values', 'keepDiag' arguments;
41                    speed up Q %*% D %*% t(Q)
42            * tests/dpoMatrix.R: test nearPD()
43    
44    2007-12-05  Doug Bates and Martin Maechler
45    
46            * R/sparseMatrix.R: xtabs(*, sparse=.) function; an extention of
47            stats::xtabs() allowing to create sparse matrices.
48    
49    2007-10-08  Martin Maechler  <maechler@stat.math.ethz.ch>
50    
51            * DESCRIPTION (Version): *-4 (released *-3 two days ago)
52    
53    2007-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
54    
55            * R/pMatrix.R: solve(<Matrix>, <pMatrix>)
56    
57    2007-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
58    
59            * R/LU.R: solve() method for "denseLU"
60    
61    2007-10-01  Martin Maechler  <maechler@stat.math.ethz.ch>
62    
63            * DESCRIPTION (Version): 0.999375-3 preparing for release
64    
65            * R/AllGeneric.R: simplify  if(.) .. else .. for R <= 2.5.1
66    
67            * R/Matrix.R (Matrix): .Internal(matrix(..)) different for R >= 2.7.0
68    
69    2007-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
70    
71            * R/pMatrix.R (.m.mult.pMat): fix <matrix> %*% <pMatrix>,
72              thanks to Kasper Kristensen.
73            * tests/matprod.R: regression test for that.
74    
75    2007-09-23 17:32  Douglas Bates <bates@stat.wisc.edu>
76    
77            * [r4778] R/AllGeneric.R: Check R version before defining generics for
78              primitives
79    
80    2007-09-13  Martin Maechler  <maechler@stat.math.ethz.ch>
81    
82            * R/denseMatrix.R (rcond): method
83            * R/sparseQR.R (rcond): method, use x or t(x)
84    
85    2007-09-12  Martin Maechler  <maechler@stat.math.ethz.ch>
86    
87            * R/dgeMatrix.R (rcond): method: work via qr.R() for non-square
88            matrices.
89            * R/sparseMatrix.R: Ditto for all other rcond() method definitions.
90    
91            * man/rcond.Rd: mention the more general definition, and add
92            example for non-square matrices.
93    
94            * man/chol.Rd: new file, for the S4 chol() generic and all methods.
95    
96    2007-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
97    
98            * R/sparseQR.R: add qr.R() method [to be used for rcond()]
99    
100    2007-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
101    
102            * R/Matrix.R ([<-): add (Matrix,missing,ANY,Matrix) etc
103            * tests/indexing.R: add new regression for the above cases.
104    
105    2007-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
106    
107            * src/Mutils.h (__sun): clause for alloca.h on Solaris
108    
109    2007-08-16  Martin Maechler  <maechler@stat.math.ethz.ch>
110    
111            * DESCRIPTION (Date, Version): 0.999375-2
112    
113    2007-08-15  Martin Maechler  <maechler@stat.math.ethz.ch>
114    
115            * R/HBMM.R (readMM): make work for pattern matrices as well
116    
117    2007-08-14 13:07  Douglas Bates <bates@stat.wisc.edu>
118    
119            * [r4730] src/Mutils.h: declare alloca
120            * [r4734] NAMESPACE, R/AllGeneric.R, R/Csparse.R, R/HBMM.R, R/Tsparse.R,
121              R/dgCMatrix.R, R/dgTMatrix.R, R/dsCMatrix.R, R/dsTMatrix.R,
122              man/externalFormats.Rd, src/Csparse.c, src/Csparse.h, src/DEPS.mkf,
123              src/HBMM.c, src/HBMM.h, src/Mutils.h, src/SOURCES_C.mkf, src/init.c,
124              src/mmio.c, src/mmio.h: Remove deprecated function writeHB and its
125              methods; switch writeMM to use CHOLMOD code; repair readMM
126    
127    2007-08-14  Martin Maechler  <maechler@stat.math.ethz.ch>
128    
129            * R/nearPD.R, man/nearPD.Rd (nearPD): new function built on Jens
130            Oehlschlaegel's ... result type still to be discussed!
131    
132    2007-08-10  Martin Maechler  <maechler@stat.math.ethz.ch>
133    
134            * man/image-methods.Rd: new, combining all image() methods
135    
136    2007-08-09  Martin Maechler  <maechler@stat.math.ethz.ch>
137    
138            * R/dgCMatrix.R: define qr() and lu() methods for "sparseMatrix"
139            to work via dgC...
140    
141            * R/Matrix.R (Matrix): special treatment for "table" (S3)
142    
143    2007-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
144    
145            * R/dgTMatrix.R (image): change defaults to
146                    aspect = "iso", colorkey = FALSE
147    
148    2007-08-06  Martin Maechler  <maechler@stat.math.ethz.ch>
149    
150            * src/dsyMatrix.c (dsyMatrix_matrix_mm): 'b' might be matrix;
151            must copy its *expanded* x slot before LAPACK call.
152    
153            * tests/matprod.R: test the last days' changes.
154    
155    2007-08-06 16:43  Douglas Bates <bates@stat.wisc.edu>
156    
157            * [r4712] inst/include/Matrix_stubs.c: Change R_cholmod_printf in stubs
158              as well as in sources
159            * [r4713] src/dsyMatrix.c: Duplicate the contents of the RHS before
160              Lapack call
161    
162    2007-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
163    
164            * R/Matrix.R (%*%, crossprod, tcrossprod): add method for
165                    ("Matrix", "matrix") which is needed in some cases.
166            Ditto for solve().
167    
168            * R/colSums.R (.as.dge.Fun): need ddenseMatrix methods to avoid
169            infinite recursion in dispatch for some cases.
170    
171    2007-08-02 08:48  Martin Maechler <maechler@stat.math.ethz.ch>
172    
173            * [r4693] src/chm_common.c: R_cholmod_printf() instead of Rprintf() just
174              so pointers match
175    
176    2007-08-02  Martin Maechler  <maechler@stat.math.ethz.ch>
177    
178            * DESCRIPTION (Date): set ready for release -- 0.999375-1
179    
180    2007-08-01 15:44  Douglas Bates <bates@stat.wisc.edu>
181    
182            * [r4686] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
183              src/chm_common.c, src/chm_common.h: Change API for
184              numeric_as_chm_dense and N_AS_CHM_DN
185    
186    2007-08-01  Martin Maechler  <maechler@stat.math.ethz.ch>
187    
188            * src/dtrMatrix.c (dtrMatrix_matrix_mm): fix dimensionality check (!)
189            * tests/matprod.R: regr.test for it
190    
191    2007-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
192    
193            * R/dMatrix.R: fix from Brian for   Math2(., digits = "missing")
194            * tests/group-methods.R: and regression-test it
195    
196    2007-07-19 19:45  Douglas Bates <bates@stat.wisc.edu>
197    
198            * [r4642] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
199              inst/include/cholmod.h, src/chm_common.c, src/init.c: Export
200              triplet_to_sparse, documentation, use typedefs
201    
202    2007-07-18  Martin Maechler  <maechler@stat.math.ethz.ch>
203    
204            * man/dpoMatrix-class.Rd: added 'corMatrix' example
205    
206            * src/dsyMatrix.[ch] (dsyMatrix_as_matrix): new 'keep_dimnames' arg
207            * src/dtrMatrix.[ch] (dtrMatrix_as_matrix): ditto
208            * src/init.c, R/dsyMatrix.R, R/dtrMatrix.R, R/lgTMatrix.R: ditto
209    
210            * R/lsparseMatrix.R: bug fix in "all" method
211            * R/Ops.R (.do.Logic.lsparse): "|" bug in borderline case
212    
213            * R/dsyMatrix.R (coerce->dsTMatrix): (i,j) slots should *not* have names
214            * R/ngTMatrix.R (coerce->ngTMatrix): ditto;
215                    + matrix |-> nMatrix coercion
216            * R/pMatrix.R: + setAs()  to dMatrix and from nMatrix
217            * man/pMatrix-class.Rd: ditto
218    
219            * R/Matrix.R (Summary): method for non-dMatrix
220    
221            * tests/Class+Meth.R (extraValid): new check about "dirty" slots
222            * tests/Class+Meth.R (tstMatrixClass): test norm(.);
223                    test all Summary methods.
224    
225    2007-07-16  Martin Maechler  <maechler@stat.math.ethz.ch>
226    
227            * R/dgeMatrix.R (norm, rcond): methods for 'matrix'
228    
229    2007-07-14  Martin Maechler  <maechler@stat.math.ethz.ch>
230    
231            * R/sparseMatrix.R (norm): simple methods for sparseMatrix
232    
233            * R/pMatrix.R (t?crossprod): methods for pMatrix
234    
235    2007-07-10  Douglas Bates  <bates@stat.wisc.edu>
236    
237            * src/dgeMatrix.c (dgeMatrix_colsums): Get the logic straight.
238    
239    2007-07-09 20:45  Douglas Bates <bates@stat.wisc.edu>
240    
241            * [r4579] src/dgeMatrix.c: Untangle horrible code in dgeMatrix_colsums
242              trying to fix a subtle bug - which has been somewhere else.
243    
244    2007-07-09 19:43  Martin Maechler <maechler@stat.math.ethz.ch>
245    
246            * [r4578] src/dgeMatrix.c: "cleaned" dgeMatrix_colsums() - but did not
247              solve the bug
248    
249    2007-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
250    
251            * src/dgCMatrix.c (compressed_to_TMatrix):
252    
253    2007-07-07  Martin Maechler  <maechler@stat.math.ethz.ch>
254    
255            * src/Csparse.c (Rsparse_validate): new, to have some validity
256            checking for RsparseMatrix
257            * src/dgCMatrix.c (xRMatrix_validate): ditto
258            * src/dtCMatrix.c (tRMatrix_validate): ditto
259    
260    2007-07-07  Douglas Bates <bates@stat.wisc.edu>
261    
262            * [r4567] R/AllClass.R: Slots already in RsparseMatrix were redefined in
263              lgRMatrix
264            * [r4568] DESCRIPTION: Prepare for bug-fix release
265            * [r4570] src/CHOLMOD/Check/cholmod_write.c: Include cholmod_matrixops.h
266              for declaration of cholmod_symmetry
267    
268    2007-07-06  Martin Maechler  <maechler@stat.math.ethz.ch>
269    
270            * DESCRIPTION (Version): 0.999375 merged into the trunk; ready for
271            release.
272    
273    2007-07-06 14:11  Douglas Bates <bates@stat.wisc.edu>
274    
275            * [r4559] src/iohb.c, src/iohb.h: Remove Harwell-Boeing input/output
276              functions - no longer used
277            * [r4560] src/HBMM.c, src/Mutils.c, src/dgTMatrix.c, src/dgeMatrix.c,
278              src/dspMatrix.c, src/dsyMatrix.c, src/dtCMatrix.c,
279              src/factorizations.c, src/sparseQR.c: Replace most calls to Calloc by
280              Alloca
281    
282    2007-07-06 13:14  Martin Maechler <maechler@stat.math.ethz.ch>
283    
284            * [r4558] inst/doc/Comparisons.Rnw, src/CHMfactor.c, src/Csparse.c,
285              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dense.c,
286              src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c, src/sparseQR.c,
287              src/t_gCMatrix_colSums.c: more R_CheckStack()s
288    
289    2007-07-05 18:12  Douglas Bates <bates@stat.wisc.edu>
290    
291            * [r4550] inst/include/Matrix.h: Add the macro N_AS_CHM_DN to "alloca"
292              the required amount of memory then call M_numeric_as_chm_dense.
293            * [r4556] src/Mutils.h, src/dgCMatrix.c: Define and use the Alloca macro
294              (like Calloc but calling alloca)
295    
296    2007-07-05  Martin Maechler  <maechler@stat.math.ethz.ch>
297    
298            * R/sparseMatrix.R (printSpMatrix): renamed from prSpMatrix()
299            and extended with more sophisticated 'col.names' option.
300            * NAMESPACE: export  printSparseMatrix()
301            * man/printSpMatrix.Rd: document, incl. examples
302    
303    2007-07-04 16:21  Douglas Bates <bates@stat.wisc.edu>
304    
305            * [r4543] src/cs_utils.c, src/cs_utils.h, src/dgCMatrix.c,
306              src/dtCMatrix.c, src/sparseQR.c: CSP typedef for *cs and macro
307              AS_CSP. API change - pass the empty structure to Matrix_as_cs.
308    
309    2007-07-04  Martin Maechler  <maechler@stat.math.ethz.ch>
310    
311            * DESCRIPTION (Version): 0.99875-4
312    
313            * tests/Class+Meth.R (tstMatrixClass): add dimnames, and hence test
314            some dimnames perservation.
315    
316            * R/dsTMatrix.R (t-method): keep dimnames
317            * R/dtTMatrix.R:  ditto
318    
319            * R/sparseMatrix.R (prSpMatrix): print colnames when non-trivial
320            and ncol(.) < 10
321    
322            * src/cs_utils.c: drop check_class() and use Matrix_check_class()
323            from Mutils.h
324    
325            * src/lgCMatrix.c ([ln]csc_to_matrix): no longer lose dimnames,
326            e.g. in as(<ngCMatrix>, "matrix")
327    
328    2007-07-01 13:27  Douglas Bates <bates@stat.wisc.edu>
329    
330            * [r4529] .: Create a branch for the API changes from the 0.99875
331              series to the 0.999375 series
332            * [r4530] DESCRIPTION, inst/include/Matrix.h,
333              inst/include/Matrix_stubs.c, src/CHMfactor.c, src/Csparse.c,
334              src/Mutils.h, src/Tsparse.c, src/chm_common.c, src/chm_common.h,
335              src/dense.c, src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c,
336              src/t_gCMatrix_colSums.c: API change - pass the empty structure to the
337              as_cholmod_x functions
338    
339    2007-06-30 09:05  Martin Maechler <maechler@stat.math.ethz.ch>
340    
341            * [r4527] trunk/Matrix/DESCRIPTION, trunk/Matrix/NAMESPACE,
342              trunk/Matrix/inst/doc/Comparisons.Rnw: add session- and hardware-info
343              to Comparisons
344    
345    >>>>>>> .merge-right.r4561
346    2007-06-29  Martin Maechler  <maechler@stat.math.ethz.ch>
347    
348            * DESCRIPTION (Version): 0.99875-3 ready to be released.
349    
350            * R/sparseMatrix.R (spMatrix): make spMatrix(3,4) working
351    
352            * R/AllGeneric.R: set "Math" (and "Math2") group generics in a way
353            that should also work in a future version of R.
354    
355    2007-06-21  Martin Maechler  <maechler@stat.math.ethz.ch>
356    
357            * NAMESPACE, R/AllClass.R: "xsparseVector" class union.
358    
359            * R/sparseVector.R: more *sparseVector coercions, notably for
360            non - double ones.
361    
362    2007-06-19  Martin Maechler  <maechler@stat.math.ethz.ch>
363    
364            * R/colSums.R: new file for all (col|row)(Sums|Means) methods,
365              notably the new ones building on the new .Call(.)s:
366    
367            * src/dgCMatrix.c (DEF_gCMatrix_COLSUMS): use to define
368            all 4 of [dlin]gCMatrix_colSums().
369    
370    2007-06-18 16:12  Douglas Bates <bates@stat.wisc.edu>
371    
372            * [r4472] src/Syms.h, src/init.c: Added Matrix_lengthSym
373            * [r4473] src/dgCMatrix.c: Modified dgCMatrix_colSums for sparseVector
374              result
375    
376    2007-06-16  Martin Maechler  <maechler@stat.math.ethz.ch>
377    
378            * R/kronecker.R: fix typo (could lead to inf.recursion)
379            * test/simple.R: testing that
380    
381            * R/sparseMatrix.R (prSpMatrix): change to be used as print()
382            method as well (which can have arguments, show() can't).
383    
384    2007-06-16 15:52  Douglas Bates <bates@stat.wisc.edu>
385    
386            * [r4466] R/dgCMatrix.R, src/dgCMatrix.c, src/dgCMatrix.h, src/init.c:
387              added dgCMatrix_colSums for [col,row][Sums,Means]
388    
389    2007-06-15 23:15  Douglas Bates <bates@stat.wisc.edu>
390    
391            * [r4460] R/sparseMatrix.R, man/dgCMatrix-class.Rd, src/dgCMatrix.c,
392              src/dgCMatrix.h, src/init.c: added lm.fit.sparse (unexported),
393              coercion of "factor" to "dgCMatrix" and dgCMatrix_cholsol
394            * [r4461] R/AllClass.R, man/sparseMatrix-class.Rd: draft "indicators"
395              class
396            * [r4463] R/sparseMatrix.R, man/dgCMatrix-class.Rd,
397              man/sparseMatrix-class.Rd: Don't need an "indicators" class - use the
398              row names to store the levels - duh!  Added an example.
399    
400    2007-06-14  Martin Maechler  <maechler@stat.math.ethz.ch>
401    
402            * src/Csparse.c (Csparse_validate): check for *repeated* entries
403            thanks to example from Christian Buchta; with a test here:
404            * tests/simple.R:
405    
406    2007-06-07  Martin Maechler  <maechler@stat.math.ethz.ch>
407    
408            * R/Auxiliaries.R (callGeneric): another fix, needed for some cases
409            of colSums(*, sparseResult = TRUE)
410    
411    2007-06-06  Martin Maechler  <maechler@stat.math.ethz.ch>
412    
413            * R/lsparseMatrix.R, R/ldenseMatrix.R (all, any): change default to
414            'na.rm = FALSE' as "everywhere" else in R.
415    
416    2007-06-05 Douglas Bates <bates@stat.wisc.edu>
417    
418            * [r4421] src/CSparse_install.sh: Modify for new organization of
419              CSparse package
420            * [r4425] src/UFsparse_download.sh: Update to version 3.0.0 of
421              SuiteSparse
422            * [r4426] src/Makefile: add ./UFconfig to the include path for
423              compilation
424            * [r4427] src/cs.[ch]: update to CSparse version 2.2.0
425            * [r4428] inst/doc/UFsparse/* src/{AMD,CHOLMOD,COLAMD}/*
426              src/UFconfig/UFconfig.h: Update to version 3.0.0 of SuiteSparse
427    
428    2007-06-05  Martin Maechler  <maechler@stat.math.ethz.ch>
429    
430            * R/Auxiliaries.R (emptyColnames): + argument msg.if.not.empty, used in
431            * R/sparseMatrix.R (prSpMatrix): now gives a message about
432            suppressed column names.
433    
434    2007-06-04 17:13  Douglas Bates <bates@stat.wisc.edu>
435    
436            * [r4418] src/Csparse.c, src/HBMM.c, src/Mutils.c, src/Mutils.h,
437              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dgCMatrix.c,
438              src/dgeMatrix.c, src/dpoMatrix.c, src/dpoMatrix.h, src/dppMatrix.c,
439              src/dppMatrix.h, src/dsCMatrix.c, src/dspMatrix.c, src/dspMatrix.h,
440              src/dsyMatrix.c, src/dsyMatrix.h, src/dtpMatrix.c, src/dtrMatrix.c:
441              Remove warnings after change to const char* CHAR
442    
443    2007-06-04 17:11  Douglas Bates <bates@stat.wisc.edu>
444    
445            * [r4417] inst/include/Matrix_stubs.c, inst/include/cholmod.h: Corrected
446              type of M_cholmod_ssmult
447    
448    2007-06-03 14:42  Douglas Bates <bates@stat.wisc.edu>
449    
450            * [r4412] inst/include/Matrix_stubs.c, inst/include/cholmod.h,
451              src/init.c: Yet another cholmod export - cholmod_ssmult
452    
453    2007-05-23  Martin Maechler  <maechler@stat.math.ethz.ch>
454    
455            * NAMESPACE: exported drop0(), since
456            * man/drop0.Rd: I have seen several cases, I really wanted to use
457            it, so our users may want too.
458    
459    2007-05-22  Martin Maechler  <maechler@stat.math.ethz.ch>
460    
461            * man/colSums.Rd: separately document colSums() etc, since these
462            have the extra argument 'sparseResult'.
463    
464    2007-05-21  Martin Maechler  <maechler@stat.math.ethz.ch>
465    
466            * R/sparseMatrix.R (spMatrix): utility (T)sparse Matrix constructor;
467            * man/spMatrix.Rd: docu., including examples
468    
469            * R/Auxiliaries.R (sp.colMeans): etc, using a patched callGeneric(),
470            in order to make colMeans() etc fast *and* correct.
471            * R/sparseVector.R (replSPvec): "[<-" functionality for
472            sparseVectors; tested in
473            * tests/simple.R:
474    
475    2007-05-19  Martin Maechler  <maechler@stat.math.ethz.ch>
476    
477            * R/sparseMatrix.R (print.sparseSummary): and summary() method for
478            (very) sparse Matrices; output similar to Matlab's print().
479    
480    2007-05-17  Douglas Bates  <bates@stat.wisc.edu>
481    
482            * src/HBMM.c (Matrix_writeMatrixMarket): Write 1-based, not
483            0-based, indices (Jose Quesada <quesada@gmail.com>).
484    
485    2007-05-16  Douglas Bates  <bates@stat.wisc.edu>
486    
487            * R/CHMfactor.R: Added solve methods for a CHMfactor object.
488    
489    2007-05-16  Martin Maechler  <maechler@stat.math.ethz.ch>
490    
491            * R/Auxiliaries.R (sparsapply): new utility, much faster than
492            tapply1() for large sparse matrices.
493    
494    2007-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
495    
496            * R/Matrix.R (dim<-): reshape now via sparseVector.
497    
498            * R/sparseVector.R: methods and function for
499            * R/AllClass.R: new "sparseVector" class and daughters.
500            * NAMESPACE: export new classes
501    
502    2007-05-14  Martin Maechler  <maechler@stat.math.ethz.ch>
503    
504            * DESCRIPTION (Version): 0.99875-1
505            * src/Makefile.win: also remove Lapack code from here (cf. 04-25).
506    
507    2007-05-11  Martin Maechler  <maechler@stat.math.ethz.ch>
508    
509            * R/Tsparse.R ([, Tsparse): fix last case: *duplicated*, symmetric
510            indexing
511            * tests/indexing.R: test set for that.
512    
513    2007-05-08  Martin Maechler  <maechler@stat.math.ethz.ch>
514    
515            * R/Tsparse.R (replTmat): fix the case of *duplicated* index
516            entries.
517            * tests/indexing.R(out): add regression test for it
518    
519    2007-04-30  Martin Maechler  <maechler@stat.math.ethz.ch>
520    
521            * R/(l(dense|sparse))?Matrix.R (!): use 'x', not 'e1' as argument
522            name for "!" method definitions.
523    
524    2007-04-26  Martin Maechler  <maechler@stat.math.ethz.ch>
525    
526            * R/Tsparse.R (intI): new utility, used for "[" :
527                    Cleanup up there, and fixes for duplicated indices - more TODO!
528    
529            * tests/indexing.R(out): more tests
530    
531    2007-04-25  Douglas Bates  <bates@stat.wisc.edu>
532    
533            * DESCRIPTION,src/Makefile: require R>= 2.5.0 and remove Lapack
534            code that is now part of the R Lapack library.
535    
536            * src/init.c,inst/include/{Matrix_stubs.c,cholmod.h}:export
537            cholmod_factorize_p (used in lme4 for GLMMs and NLMMs).
538    
539    2007-04-21  Martin Maechler  <maechler@stat.math.ethz.ch>
540    
541            * R/Matrix.R (image): method for all Matrices, not just sparse ones.
542    
543    2007-04-17  Martin Maechler  <maechler@stat.math.ethz.ch>
544    
545            * R/Auxiliaries.R (tapply1): unname(.) -> colSums() etc don't end
546            up with extraneous names '0'...'<n-1>'
547    
548    2007-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
549    
550            * R/dgTMatrix.R (mat2dgT): care about NAs
551    
552    2007-04-11  Martin Maechler  <maechler@stat.math.ethz.ch>
553    
554            * R/kronecker.R: triangularity preserving methods
555    
556    2007-03-27  Martin Maechler  <maechler@stat.math.ethz.ch>
557    
558            * R/kronecker.R: new file collecting kronecker() methods in one
559                    place.  Goal: become much faster!
560    
561    2007-03-23  Martin Maechler  <maechler@stat.math.ethz.ch>
562    
563            * src/dtCMatrix.c (dtCMatrix_solve): use the new code from Kasper
564            Kristensen based cs_spsolve() instead of _lsolve & _usolve which
565            can be much faster.
566    
567            * tests/matprod.R: add regression tests for these (upper & lower).
568    
569    2007-03-19  Martin Maechler  <maechler@stat.math.ethz.ch>
570    
571            * R/Matrix.R (diff): method for our Matrices.
572    
573            * R/sparseMatrix.R (isDiagonal): check dim()!
574    
575    2007-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
576    
577            * R/Matrix.R (dim<-): new method for "reshape()" built on a
578            proposal from Tamas Papp.
579    
580    2007-03-16  Martin Maechler  <maechler@stat.math.ethz.ch>
581    
582            * R/AllGeneric.R: remove all  if(!isGeneric(.))  clauses
583    
584            * R/zzz.R (.onLoad, .onUnload): do *not* leave bind_activation(TRUE);
585            rather define and export  cBind() and rBind() only.
586            --> useRs *must* change code that used to have cbind()/rbind() !!
587    
588            * R/bind.R: change tests from cbind() to cBind() and similarly to rBind()
589            * R/bind.Rout.save: ditto
590    
591    2007-02-16  Douglas Bates  <bates@r-project.org>
592    
593            * DESCRIPTION (Date, Version): 0.9975-11 with new date
594            * src/dgCMatrix.c (R_to_CMatrix, compressed_to_TMatrix): remove
595            const modifier on declaration of the array 'valid'
596    
597    2007-02-12  Douglas Bates  <bates@stat.wisc.edu>
598    
599            * R/CHMfactor.R: Add image method (coercion to sparseMatrix).
600    
601    2007-02-05  Martin Maechler  <maechler@stat.math.ethz.ch>
602    
603            * DESCRIPTION (Date, Version): 0.9975-10 with new date.
604    
605            * R/Ops.R (Arith): make sure Csparse o Csparse also works for e.g. ntCMatrix
606            * tests/simple.R: test the above and some of these coercions:
607    
608            * R/nsparseMatrix.R: coercing "Csparse" to "lsparseMatrix";
609                    be careful to avoid infinite recursion, using new coercions in
610            * R/ngCMatrix.R and nsC... and ntC...
611            * R/lsparseMatrix.R: ditto
612    
613            * R/SparseM-conv.R: more conversion, notably for triplet matrices.
614    
615            * src/dgCMatrix.c (R_to_C_Matrix): port Doug's fix and
616            * R/Rsparse.R: reactivate .Call()s
617    
618            * tests/Class+Meth.R: a bit more on actual classes
619    
620    2007-02-04  Douglas Bates  <bates@stat.wisc.edu>
621    
622            * src/dgCMatrix.c (compressed_to_TMatrix): fix memory bug using strdup()
623    
624    2007-02-03  Martin Maechler  <maechler@stat.math.ethz.ch>
625    
626            * DESCRIPTION (Version): 0.9975-10 to upload
627    
628            * tests/Class+Meth.R (tstMatrixClass): require coercions to
629            specific classes less unconditionally.
630    
631            * R/Auxiliaries.R: get rid of as_Tsparse() and as_Rsparse()
632    
633            * R/Tsparse.R (triu): etc, use as(*, "TsparseMatrix") instead of as_Tsparse()
634    
635            * R/Rsparse.R (.R.2.T): R-level workaround using compressed_to_TMatrix.
636            * R/Rsparse.R (.R.2.C): R-level workaround since C-level
637            R_to_CMatrix segfaults on one platform.
638            Eliminate most coercion method to *specific* classes, and replace
639            with virtual classes coercions.
640    
641    
642    2007-02-01  Martin Maechler <maechler@stat.math.ethz.ch>
643    
644            * src/init.c: export the CHM...._validate() placeholders, since
645            they *are* called.
646    
647            * tests/Class+Meth.R (classCanCoerce): and starting to test
648            all as(<from>, <to>)
649    
650    2007-01-30  Martin Maechler  <maechler@stat.math.ethz.ch>
651    
652            * R/Tsparse.R ([): more care when subsetting triangular Tsparse
653            * tests/indexing.R: tested now
654            * tests/indexing.Rout.save: updated
655    
656            * src/Csparse.c (Csparse_to_dense): use Rkind = -1 for PATTERN to
657            * src/chm_common.c (chm_dense_to_SEXP): return "ngeMatrix" when
658            appropriate.
659    
660            * NAMESPACE: export a trivial
661            * R/Matrix.R: drop() Matrix-method
662    
663            * R/AllClass.R: moved all prototypes to virtual super classes.
664    
665            * R/Rsparse.R: many more coercions to have less exceptions in
666            * tests/Class+Meth.R:
667    
668            * R/Ops.R (Compare): tweak for case with NA
669            * tests/simpl.R: hence another 'FIXME' eliminated
670    
671    2007-01-29  Martin Maechler  <maechler@stat.math.ethz.ch>
672    
673            * R/diagMatrix.R (solve): the obvious methods for diagonalMatrix
674            objects.
675    
676            * tests/Class+Meth.R (tstMatrixClass): now testing diag(), nnzero(),
677              and more of "!", "&", "|", all, any; coercions
678    
679            * R/Rsparse.R: many coercions (which enable quite a few other
680            methods), thanks to enhancements in
681            * src/dgCMatrix.c (R_to_CMatrix): new, and
682            * src/dgCMatrix.c (compressed_to_TMatrix): now for (d,l,n) ,
683            symmetric & triangular and ..RMatrix objects.
684    
685            * src/TMatrix_as.c (Matrix_T_as_DENSE,Matrix_T_as_GENERAL):
686            renamed file from src/dsTMatrix.c;
687            now dealing with symmetric and triangular Tsparse coercions, both
688            to dense and general.
689    
690    2007-01-27  Martin Maechler  <maechler@stat.math.ethz.ch>
691    
692            * src/dsTMatrix.c: has now "l" and "n" methods besides the "d" ones.
693    
694            * R/Ops.R (Arith): <dgCMatrix> o <numeric> now remains sparse
695            where sensible when the <numeric> is of length > 1.
696    
697    2007-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
698    
699            * R/Matrix.R ([<-): for M[] <- value: fix length
700    
701    2007-01-25  Martin Maechler  <maechler@stat.math.ethz.ch>
702    
703            * R/Auxiliaries.R (n2l_Matrix): new, to be used in
704            * R/ndenseMatrix.R: new coercions n* -> l*
705    
706    2007-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
707    
708            * R/triangularMatrix.R: new file; simple triu() and tril() methods.
709    
710            * R/Ops.R ("Logic"): and other "Ops", many updates
711    
712    2007-01-18  Martin Maechler  <maechler@stat.math.ethz.ch>
713    
714            * src/Mutils.h (SET_DimNames): new utility
715    
716            * R/Auxiliaries.R (nnzero): improved and now exported via
717    
718            * NAMESPACE: + nnzero(); length() == prod(dim(.)) method for all "Matrix" objects
719    
720    2007-01-17  Martin Maechler  <maechler@stat.math.ethz.ch>
721    
722            * R/diagMatrix.R (!): fix typo.
723    
724    2007-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
725    
726            * R/Auxiliaries.R (as_Csparse): and quite a few others:
727                    allow to pass class definition --> speedup
728            * R/sparseMatrix.R: apply the above
729    
730            * R/Csparse.R: coercion Csparse* to dense* now preserves shape properties.
731    
732            * src/Mutils.h (mMatrix_as_geMatrix): new, based on
733            * src/Mutils.c (dup_mMatrix_as_geMatrix): new; generalization of
734            old dup_mMatrix_as_dgeMatrix), eliminating a long-standing "FIXME".
735    
736            * src/dense.c (dense_to_Csparse): use new mMatrix_as_geMatrix()
737    
738            * R/denseMatrix.R (.dense2C): based on dense_to_Csparse: name it,
739            and use it for "sparse*" as well, since it's faster than the
740            as_Csparse(.) way.
741    
742    2007-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
743    
744            * R/Ops.R ("Logic"): more methods, notably an  <lgC> o <lgC> one.
745    
746    2007-01-12  Martin Maechler  <maechler@stat.math.ethz.ch>
747    
748            * R/Tsparse.R (.TM.repl.i.2col): new internal function to be used
749            as method for   M[ ij ] <- v
750            * R/Csparse.R:: go via Tsparse for "M[ij] <- v"
751    
752            * R/Ops.R: "Compare" for (C|R)sparse: need pointer slot for all
753            FALSE answer
754    
755            * R/Csparse.R (replCmat): fix the "all non-zero" case with reordering
756            * tests/indexing.R: test it, and some of the above
757    
758    2007-01-05  Martin Maechler  <maechler@stat.math.ethz.ch>
759    
760            * R/Auxiliaries.R (is_duplicatedT): new utility
761    
762  2007-01-05  Douglas Bates  <bates@stat.wisc.edu>  2007-01-05  Douglas Bates  <bates@stat.wisc.edu>
763    
764          * src/init.c (R_init_Matrix): export cholmod_scale          * src/init.c (R_init_Matrix): export cholmod_scale
765    
766    2006-12-30  Martin Maechler  <maechler@stat.math.ethz.ch>
767    
768            * R/zzz.R (tmp): for R >= 2.5.0, extend formals of our
769            base::as.matrix to (x, ...)
770    
771  2006-12-28  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-12-28  Martin Maechler  <maechler@stat.math.ethz.ch>
772    
773          * R/Ops.R ("Arith" etc): move almost all "Ops" methods to new R          * R/Ops.R ("Arith" etc): move almost all "Ops" methods to new R

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