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revision 1767, Mon Feb 5 16:53:17 2007 UTC revision 2043, Sat Aug 11 03:18:26 2007 UTC
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1    2007-08-10  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * man/image-methods.Rd: new, combining all image() methods
4    
5    2007-08-09  Martin Maechler  <maechler@stat.math.ethz.ch>
6    
7            * R/dgCMatrix.R: define qr() and lu() methods for "sparseMatrix"
8            to work via dgC...
9    
10            * R/Matrix.R (Matrix): special treatment for "table" (S3)
11    
12    2007-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
13    
14            * R/dgTMatrix.R (image): change defaults to
15                    aspect = "iso", colorkey = FALSE
16    
17    2007-08-06  Martin Maechler  <maechler@stat.math.ethz.ch>
18    
19            * src/dsyMatrix.c (dsyMatrix_matrix_mm): 'b' might be matrix;
20            must copy its *expanded* x slot before LAPACK call.
21    
22            * tests/matprod.R: test the last days' changes.
23    
24    2007-08-06 16:43  Douglas Bates <bates@stat.wisc.edu>
25    
26            * [r4712] inst/include/Matrix_stubs.c: Change R_cholmod_printf in stubs
27              as well as in sources
28    
29    2007-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
30    
31            * R/Matrix.R (%*%, crossprod, tcrossprod): add method for
32                    ("Matrix", "matrix") which is needed in some cases.
33            Ditto for solve().
34    
35            * R/colSums.R (.as.dge.Fun): need ddenseMatrix methods to avoid
36            infinite recursion in dispatch for some cases.
37    
38    2007-08-02 08:48  Martin Maechler <maechler@stat.math.ethz.ch>
39    
40            * [r4693] src/chm_common.c: R_cholmod_printf() instead of Rprintf() just
41              so pointers match
42    
43    2007-08-02  Martin Maechler  <maechler@stat.math.ethz.ch>
44    
45            * DESCRIPTION (Date): set ready for release -- 0.999375-1
46    
47    2007-08-01 15:44  Douglas Bates <bates@stat.wisc.edu>
48    
49            * [r4686] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
50              src/chm_common.c, src/chm_common.h: Change API for
51              numeric_as_chm_dense and N_AS_CHM_DN
52    
53    2007-08-01  Martin Maechler  <maechler@stat.math.ethz.ch>
54    
55            * src/dtrMatrix.c (dtrMatrix_matrix_mm): fix dimensionality check (!)
56            * tests/matprod.R: regr.test for it
57    
58    2007-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
59    
60            * R/dMatrix.R: fix from Brian for   Math2(., digits = "missing")
61            * tests/group-methods.R: and regression-test it
62    
63    2007-07-19 19:45  Douglas Bates <bates@stat.wisc.edu>
64    
65            * [r4642] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
66              inst/include/cholmod.h, src/chm_common.c, src/init.c: Export
67              triplet_to_sparse, documentation, use typedefs
68    
69    2007-07-18  Martin Maechler  <maechler@stat.math.ethz.ch>
70    
71            * man/dpoMatrix-class.Rd: added 'corMatrix' example
72    
73            * src/dsyMatrix.[ch] (dsyMatrix_as_matrix): new 'keep_dimnames' arg
74            * src/dtrMatrix.[ch] (dtrMatrix_as_matrix): ditto
75            * src/init.c, R/dsyMatrix.R, R/dtrMatrix.R, R/lgTMatrix.R: ditto
76    
77            * R/lsparseMatrix.R: bug fix in "all" method
78            * R/Ops.R (.do.Logic.lsparse): "|" bug in borderline case
79    
80            * R/dsyMatrix.R (coerce->dsTMatrix): (i,j) slots should *not* have names
81            * R/ngTMatrix.R (coerce->ngTMatrix): ditto;
82                    + matrix |-> nMatrix coercion
83            * R/pMatrix.R: + setAs()  to dMatrix and from nMatrix
84            * man/pMatrix-class.Rd: ditto
85    
86            * R/Matrix.R (Summary): method for non-dMatrix
87    
88            * tests/Class+Meth.R (extraValid): new check about "dirty" slots
89            * tests/Class+Meth.R (tstMatrixClass): test norm(.);
90                    test all Summary methods.
91    
92    2007-07-16  Martin Maechler  <maechler@stat.math.ethz.ch>
93    
94            * R/dgeMatrix.R (norm, rcond): methods for 'matrix'
95    
96    2007-07-14  Martin Maechler  <maechler@stat.math.ethz.ch>
97    
98            * R/sparseMatrix.R (norm): simple methods for sparseMatrix
99    
100            * R/pMatrix.R (t?crossprod): methods for pMatrix
101    
102    2007-07-10  Douglas Bates  <bates@stat.wisc.edu>
103    
104            * src/dgeMatrix.c (dgeMatrix_colsums): Get the logic straight.
105    
106    2007-07-09 20:45  Douglas Bates <bates@stat.wisc.edu>
107    
108            * [r4579] src/dgeMatrix.c: Untangle horrible code in dgeMatrix_colsums
109              trying to fix a subtle bug - which has been somewhere else.
110    
111    2007-07-09 19:43  Martin Maechler <maechler@stat.math.ethz.ch>
112    
113            * [r4578] src/dgeMatrix.c: "cleaned" dgeMatrix_colsums() - but did not
114              solve the bug
115    
116    2007-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
117    
118            * src/dgCMatrix.c (compressed_to_TMatrix):
119    
120    2007-07-07  Martin Maechler  <maechler@stat.math.ethz.ch>
121    
122            * src/Csparse.c (Rsparse_validate): new, to have some validity
123            checking for RsparseMatrix
124            * src/dgCMatrix.c (xRMatrix_validate): ditto
125            * src/dtCMatrix.c (tRMatrix_validate): ditto
126    
127    2007-07-07  Douglas Bates <bates@stat.wisc.edu>
128    
129            * [r4567] R/AllClass.R: Slots already in RsparseMatrix were redefined in
130              lgRMatrix
131            * [r4568] DESCRIPTION: Prepare for bug-fix release
132            * [r4570] src/CHOLMOD/Check/cholmod_write.c: Include cholmod_matrixops.h
133              for declaration of cholmod_symmetry
134    
135    2007-07-06  Martin Maechler  <maechler@stat.math.ethz.ch>
136    
137            * DESCRIPTION (Version): 0.999375 merged into the trunk; ready for
138            release.
139    
140    2007-07-06 14:11  Douglas Bates <bates@stat.wisc.edu>
141    
142            * [r4559] src/iohb.c, src/iohb.h: Remove Harwell-Boeing input/output
143              functions - no longer used
144            * [r4560] src/HBMM.c, src/Mutils.c, src/dgTMatrix.c, src/dgeMatrix.c,
145              src/dspMatrix.c, src/dsyMatrix.c, src/dtCMatrix.c,
146              src/factorizations.c, src/sparseQR.c: Replace most calls to Calloc by
147              Alloca
148    
149    2007-07-06 13:14  Martin Maechler <maechler@stat.math.ethz.ch>
150    
151            * [r4558] inst/doc/Comparisons.Rnw, src/CHMfactor.c, src/Csparse.c,
152              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dense.c,
153              src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c, src/sparseQR.c,
154              src/t_gCMatrix_colSums.c: more R_CheckStack()s
155    
156    2007-07-05 18:12  Douglas Bates <bates@stat.wisc.edu>
157    
158            * [r4550] inst/include/Matrix.h: Add the macro N_AS_CHM_DN to "alloca"
159              the required amount of memory then call M_numeric_as_chm_dense.
160            * [r4556] src/Mutils.h, src/dgCMatrix.c: Define and use the Alloca macro
161              (like Calloc but calling alloca)
162    
163    2007-07-05  Martin Maechler  <maechler@stat.math.ethz.ch>
164    
165            * R/sparseMatrix.R (printSpMatrix): renamed from prSpMatrix()
166            and extended with more sophisticated 'col.names' option.
167            * NAMESPACE: export  printSparseMatrix()
168            * man/printSpMatrix.Rd: document, incl. examples
169    
170    2007-07-04 16:21  Douglas Bates <bates@stat.wisc.edu>
171    
172            * [r4543] src/cs_utils.c, src/cs_utils.h, src/dgCMatrix.c,
173              src/dtCMatrix.c, src/sparseQR.c: CSP typedef for *cs and macro
174              AS_CSP. API change - pass the empty structure to Matrix_as_cs.
175    
176    2007-07-04  Martin Maechler  <maechler@stat.math.ethz.ch>
177    
178            * DESCRIPTION (Version): 0.99875-4
179    
180            * tests/Class+Meth.R (tstMatrixClass): add dimnames, and hence test
181            some dimnames perservation.
182    
183            * R/dsTMatrix.R (t-method): keep dimnames
184            * R/dtTMatrix.R:  ditto
185    
186            * R/sparseMatrix.R (prSpMatrix): print colnames when non-trivial
187            and ncol(.) < 10
188    
189            * src/cs_utils.c: drop check_class() and use Matrix_check_class()
190            from Mutils.h
191    
192            * src/lgCMatrix.c ([ln]csc_to_matrix): no longer lose dimnames,
193            e.g. in as(<ngCMatrix>, "matrix")
194    
195    2007-07-01 13:27  Douglas Bates <bates@stat.wisc.edu>
196    
197            * [r4529] .: Create a branch for the API changes from the 0.99875
198              series to the 0.999375 series
199            * [r4530] DESCRIPTION, inst/include/Matrix.h,
200              inst/include/Matrix_stubs.c, src/CHMfactor.c, src/Csparse.c,
201              src/Mutils.h, src/Tsparse.c, src/chm_common.c, src/chm_common.h,
202              src/dense.c, src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c,
203              src/t_gCMatrix_colSums.c: API change - pass the empty structure to the
204              as_cholmod_x functions
205    
206    2007-06-30 09:05  Martin Maechler <maechler@stat.math.ethz.ch>
207    
208            * [r4527] trunk/Matrix/DESCRIPTION, trunk/Matrix/NAMESPACE,
209              trunk/Matrix/inst/doc/Comparisons.Rnw: add session- and hardware-info
210              to Comparisons
211    
212    >>>>>>> .merge-right.r4561
213    2007-06-29  Martin Maechler  <maechler@stat.math.ethz.ch>
214    
215            * DESCRIPTION (Version): 0.99875-3 ready to be released.
216    
217            * R/sparseMatrix.R (spMatrix): make spMatrix(3,4) working
218    
219            * R/AllGeneric.R: set "Math" (and "Math2") group generics in a way
220            that should also work in a future version of R.
221    
222    2007-06-21  Martin Maechler  <maechler@stat.math.ethz.ch>
223    
224            * NAMESPACE, R/AllClass.R: "xsparseVector" class union.
225    
226            * R/sparseVector.R: more *sparseVector coercions, notably for
227            non - double ones.
228    
229    2007-06-19  Martin Maechler  <maechler@stat.math.ethz.ch>
230    
231            * R/colSums.R: new file for all (col|row)(Sums|Means) methods,
232              notably the new ones building on the new .Call(.)s:
233    
234            * src/dgCMatrix.c (DEF_gCMatrix_COLSUMS): use to define
235            all 4 of [dlin]gCMatrix_colSums().
236    
237    2007-06-18 16:12  Douglas Bates <bates@stat.wisc.edu>
238    
239            * [r4472] src/Syms.h, src/init.c: Added Matrix_lengthSym
240            * [r4473] src/dgCMatrix.c: Modified dgCMatrix_colSums for sparseVector
241              result
242    
243    2007-06-16  Martin Maechler  <maechler@stat.math.ethz.ch>
244    
245            * R/kronecker.R: fix typo (could lead to inf.recursion)
246            * test/simple.R: testing that
247    
248            * R/sparseMatrix.R (prSpMatrix): change to be used as print()
249            method as well (which can have arguments, show() can't).
250    
251    2007-06-16 15:52  Douglas Bates <bates@stat.wisc.edu>
252    
253            * [r4466] R/dgCMatrix.R, src/dgCMatrix.c, src/dgCMatrix.h, src/init.c:
254              added dgCMatrix_colSums for [col,row][Sums,Means]
255    
256    2007-06-15 23:15  Douglas Bates <bates@stat.wisc.edu>
257    
258            * [r4460] R/sparseMatrix.R, man/dgCMatrix-class.Rd, src/dgCMatrix.c,
259              src/dgCMatrix.h, src/init.c: added lm.fit.sparse (unexported),
260              coercion of "factor" to "dgCMatrix" and dgCMatrix_cholsol
261            * [r4461] R/AllClass.R, man/sparseMatrix-class.Rd: draft "indicators"
262              class
263            * [r4463] R/sparseMatrix.R, man/dgCMatrix-class.Rd,
264              man/sparseMatrix-class.Rd: Don't need an "indicators" class - use the
265              row names to store the levels - duh!  Added an example.
266    
267    2007-06-14  Martin Maechler  <maechler@stat.math.ethz.ch>
268    
269            * src/Csparse.c (Csparse_validate): check for *repeated* entries
270            thanks to example from Christian Buchta; with a test here:
271            * tests/simple.R:
272    
273    2007-06-07  Martin Maechler  <maechler@stat.math.ethz.ch>
274    
275            * R/Auxiliaries.R (callGeneric): another fix, needed for some cases
276            of colSums(*, sparseResult = TRUE)
277    
278    2007-06-06  Martin Maechler  <maechler@stat.math.ethz.ch>
279    
280            * R/lsparseMatrix.R, R/ldenseMatrix.R (all, any): change default to
281            'na.rm = FALSE' as "everywhere" else in R.
282    
283    2007-06-05 Douglas Bates <bates@stat.wisc.edu>
284    
285            * [r4421] src/CSparse_install.sh: Modify for new organization of
286              CSparse package
287            * [r4425] src/UFsparse_download.sh: Update to version 3.0.0 of
288              SuiteSparse
289            * [r4426] src/Makefile: add ./UFconfig to the include path for
290              compilation
291            * [r4427] src/cs.[ch]: update to CSparse version 2.2.0
292            * [r4428] inst/doc/UFsparse/* src/{AMD,CHOLMOD,COLAMD}/*
293              src/UFconfig/UFconfig.h: Update to version 3.0.0 of SuiteSparse
294    
295    2007-06-05  Martin Maechler  <maechler@stat.math.ethz.ch>
296    
297            * R/Auxiliaries.R (emptyColnames): + argument msg.if.not.empty, used in
298            * R/sparseMatrix.R (prSpMatrix): now gives a message about
299            suppressed column names.
300    
301    2007-06-04 17:13  Douglas Bates <bates@stat.wisc.edu>
302    
303            * [r4418] src/Csparse.c, src/HBMM.c, src/Mutils.c, src/Mutils.h,
304              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dgCMatrix.c,
305              src/dgeMatrix.c, src/dpoMatrix.c, src/dpoMatrix.h, src/dppMatrix.c,
306              src/dppMatrix.h, src/dsCMatrix.c, src/dspMatrix.c, src/dspMatrix.h,
307              src/dsyMatrix.c, src/dsyMatrix.h, src/dtpMatrix.c, src/dtrMatrix.c:
308              Remove warnings after change to const char* CHAR
309    
310    2007-06-04 17:11  Douglas Bates <bates@stat.wisc.edu>
311    
312            * [r4417] inst/include/Matrix_stubs.c, inst/include/cholmod.h: Corrected
313              type of M_cholmod_ssmult
314    
315    2007-06-03 14:42  Douglas Bates <bates@stat.wisc.edu>
316    
317            * [r4412] inst/include/Matrix_stubs.c, inst/include/cholmod.h,
318              src/init.c: Yet another cholmod export - cholmod_ssmult
319    
320    2007-05-23  Martin Maechler  <maechler@stat.math.ethz.ch>
321    
322            * NAMESPACE: exported drop0(), since
323            * man/drop0.Rd: I have seen several cases, I really wanted to use
324            it, so our users may want too.
325    
326    2007-05-22  Martin Maechler  <maechler@stat.math.ethz.ch>
327    
328            * man/colSums.Rd: separately document colSums() etc, since these
329            have the extra argument 'sparseResult'.
330    
331    2007-05-21  Martin Maechler  <maechler@stat.math.ethz.ch>
332    
333            * R/sparseMatrix.R (spMatrix): utility (T)sparse Matrix constructor;
334            * man/spMatrix.Rd: docu., including examples
335    
336            * R/Auxiliaries.R (sp.colMeans): etc, using a patched callGeneric(),
337            in order to make colMeans() etc fast *and* correct.
338            * R/sparseVector.R (replSPvec): "[<-" functionality for
339            sparseVectors; tested in
340            * tests/simple.R:
341    
342    2007-05-19  Martin Maechler  <maechler@stat.math.ethz.ch>
343    
344            * R/sparseMatrix.R (print.sparseSummary): and summary() method for
345            (very) sparse Matrices; output similar to Matlab's print().
346    
347    2007-05-17  Douglas Bates  <bates@stat.wisc.edu>
348    
349            * src/HBMM.c (Matrix_writeMatrixMarket): Write 1-based, not
350            0-based, indices (Jose Quesada <quesada@gmail.com>).
351    
352    2007-05-16  Douglas Bates  <bates@stat.wisc.edu>
353    
354            * R/CHMfactor.R: Added solve methods for a CHMfactor object.
355    
356    2007-05-16  Martin Maechler  <maechler@stat.math.ethz.ch>
357    
358            * R/Auxiliaries.R (sparsapply): new utility, much faster than
359            tapply1() for large sparse matrices.
360    
361    2007-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
362    
363            * R/Matrix.R (dim<-): reshape now via sparseVector.
364    
365            * R/sparseVector.R: methods and function for
366            * R/AllClass.R: new "sparseVector" class and daughters.
367            * NAMESPACE: export new classes
368    
369    2007-05-14  Martin Maechler  <maechler@stat.math.ethz.ch>
370    
371            * DESCRIPTION (Version): 0.99875-1
372            * src/Makefile.win: also remove Lapack code from here (cf. 04-25).
373    
374    2007-05-11  Martin Maechler  <maechler@stat.math.ethz.ch>
375    
376            * R/Tsparse.R ([, Tsparse): fix last case: *duplicated*, symmetric
377            indexing
378            * tests/indexing.R: test set for that.
379    
380    2007-05-08  Martin Maechler  <maechler@stat.math.ethz.ch>
381    
382            * R/Tsparse.R (replTmat): fix the case of *duplicated* index
383            entries.
384            * tests/indexing.R(out): add regression test for it
385    
386    2007-04-30  Martin Maechler  <maechler@stat.math.ethz.ch>
387    
388            * R/(l(dense|sparse))?Matrix.R (!): use 'x', not 'e1' as argument
389            name for "!" method definitions.
390    
391    2007-04-26  Martin Maechler  <maechler@stat.math.ethz.ch>
392    
393            * R/Tsparse.R (intI): new utility, used for "[" :
394                    Cleanup up there, and fixes for duplicated indices - more TODO!
395    
396            * tests/indexing.R(out): more tests
397    
398    2007-04-25  Douglas Bates  <bates@stat.wisc.edu>
399    
400            * DESCRIPTION,src/Makefile: require R>= 2.5.0 and remove Lapack
401            code that is now part of the R Lapack library.
402    
403            * src/init.c,inst/include/{Matrix_stubs.c,cholmod.h}:export
404            cholmod_factorize_p (used in lme4 for GLMMs and NLMMs).
405    
406    2007-04-21  Martin Maechler  <maechler@stat.math.ethz.ch>
407    
408            * R/Matrix.R (image): method for all Matrices, not just sparse ones.
409    
410    2007-04-17  Martin Maechler  <maechler@stat.math.ethz.ch>
411    
412            * R/Auxiliaries.R (tapply1): unname(.) -> colSums() etc don't end
413            up with extraneous names '0'...'<n-1>'
414    
415    2007-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
416    
417            * R/dgTMatrix.R (mat2dgT): care about NAs
418    
419    2007-04-11  Martin Maechler  <maechler@stat.math.ethz.ch>
420    
421            * R/kronecker.R: triangularity preserving methods
422    
423    2007-03-27  Martin Maechler  <maechler@stat.math.ethz.ch>
424    
425            * R/kronecker.R: new file collecting kronecker() methods in one
426                    place.  Goal: become much faster!
427    
428    2007-03-23  Martin Maechler  <maechler@stat.math.ethz.ch>
429    
430            * src/dtCMatrix.c (dtCMatrix_solve): use the new code from Kasper
431            Kristensen based cs_spsolve() instead of _lsolve & _usolve which
432            can be much faster.
433    
434            * tests/matprod.R: add regression tests for these (upper & lower).
435    
436    2007-03-19  Martin Maechler  <maechler@stat.math.ethz.ch>
437    
438            * R/Matrix.R (diff): method for our Matrices.
439    
440            * R/sparseMatrix.R (isDiagonal): check dim()!
441    
442    2007-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
443    
444            * R/Matrix.R (dim<-): new method for "reshape()" built on a
445            proposal from Tamas Papp.
446    
447    2007-03-16  Martin Maechler  <maechler@stat.math.ethz.ch>
448    
449            * R/AllGeneric.R: remove all  if(!isGeneric(.))  clauses
450    
451            * R/zzz.R (.onLoad, .onUnload): do *not* leave bind_activation(TRUE);
452            rather define and export  cBind() and rBind() only.
453            --> useRs *must* change code that used to have cbind()/rbind() !!
454    
455            * R/bind.R: change tests from cbind() to cBind() and similarly to rBind()
456            * R/bind.Rout.save: ditto
457    
458    2007-02-16  Douglas Bates  <bates@r-project.org>
459    
460            * DESCRIPTION (Date, Version): 0.9975-11 with new date
461            * src/dgCMatrix.c (R_to_CMatrix, compressed_to_TMatrix): remove
462            const modifier on declaration of the array 'valid'
463    
464    2007-02-12  Douglas Bates  <bates@stat.wisc.edu>
465    
466            * R/CHMfactor.R: Add image method (coercion to sparseMatrix).
467    
468  2007-02-05  Martin Maechler  <maechler@stat.math.ethz.ch>  2007-02-05  Martin Maechler  <maechler@stat.math.ethz.ch>
469    
470            * DESCRIPTION (Date, Version): 0.9975-10 with new date.
471    
472          * R/Ops.R (Arith): make sure Csparse o Csparse also works for e.g. ntCMatrix          * R/Ops.R (Arith): make sure Csparse o Csparse also works for e.g. ntCMatrix
473          * tests/simple.R: test the above and some of these coercions:          * tests/simple.R: test the above and some of these coercions:
474    

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