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revision 1827, Wed Apr 25 22:22:41 2007 UTC revision 2048, Tue Aug 14 15:09:10 2007 UTC
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1    2007-08-14  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * R/nearPD.R, man/nearPD.Rd (nearPD): new function built on Jens
4            Oehlschlaegel's ... result type still to be discussed!
5    
6    2007-08-10  Martin Maechler  <maechler@stat.math.ethz.ch>
7    
8            * man/image-methods.Rd: new, combining all image() methods
9    
10    2007-08-09  Martin Maechler  <maechler@stat.math.ethz.ch>
11    
12            * R/dgCMatrix.R: define qr() and lu() methods for "sparseMatrix"
13            to work via dgC...
14    
15            * R/Matrix.R (Matrix): special treatment for "table" (S3)
16    
17    2007-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
18    
19            * R/dgTMatrix.R (image): change defaults to
20                    aspect = "iso", colorkey = FALSE
21    
22    2007-08-06  Martin Maechler  <maechler@stat.math.ethz.ch>
23    
24            * src/dsyMatrix.c (dsyMatrix_matrix_mm): 'b' might be matrix;
25            must copy its *expanded* x slot before LAPACK call.
26    
27            * tests/matprod.R: test the last days' changes.
28    
29    2007-08-06 16:43  Douglas Bates <bates@stat.wisc.edu>
30    
31            * [r4712] inst/include/Matrix_stubs.c: Change R_cholmod_printf in stubs
32              as well as in sources
33    
34    2007-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
35    
36            * R/Matrix.R (%*%, crossprod, tcrossprod): add method for
37                    ("Matrix", "matrix") which is needed in some cases.
38            Ditto for solve().
39    
40            * R/colSums.R (.as.dge.Fun): need ddenseMatrix methods to avoid
41            infinite recursion in dispatch for some cases.
42    
43    2007-08-02 08:48  Martin Maechler <maechler@stat.math.ethz.ch>
44    
45            * [r4693] src/chm_common.c: R_cholmod_printf() instead of Rprintf() just
46              so pointers match
47    
48    2007-08-02  Martin Maechler  <maechler@stat.math.ethz.ch>
49    
50            * DESCRIPTION (Date): set ready for release -- 0.999375-1
51    
52    2007-08-01 15:44  Douglas Bates <bates@stat.wisc.edu>
53    
54            * [r4686] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
55              src/chm_common.c, src/chm_common.h: Change API for
56              numeric_as_chm_dense and N_AS_CHM_DN
57    
58    2007-08-01  Martin Maechler  <maechler@stat.math.ethz.ch>
59    
60            * src/dtrMatrix.c (dtrMatrix_matrix_mm): fix dimensionality check (!)
61            * tests/matprod.R: regr.test for it
62    
63    2007-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
64    
65            * R/dMatrix.R: fix from Brian for   Math2(., digits = "missing")
66            * tests/group-methods.R: and regression-test it
67    
68    2007-07-19 19:45  Douglas Bates <bates@stat.wisc.edu>
69    
70            * [r4642] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
71              inst/include/cholmod.h, src/chm_common.c, src/init.c: Export
72              triplet_to_sparse, documentation, use typedefs
73    
74    2007-07-18  Martin Maechler  <maechler@stat.math.ethz.ch>
75    
76            * man/dpoMatrix-class.Rd: added 'corMatrix' example
77    
78            * src/dsyMatrix.[ch] (dsyMatrix_as_matrix): new 'keep_dimnames' arg
79            * src/dtrMatrix.[ch] (dtrMatrix_as_matrix): ditto
80            * src/init.c, R/dsyMatrix.R, R/dtrMatrix.R, R/lgTMatrix.R: ditto
81    
82            * R/lsparseMatrix.R: bug fix in "all" method
83            * R/Ops.R (.do.Logic.lsparse): "|" bug in borderline case
84    
85            * R/dsyMatrix.R (coerce->dsTMatrix): (i,j) slots should *not* have names
86            * R/ngTMatrix.R (coerce->ngTMatrix): ditto;
87                    + matrix |-> nMatrix coercion
88            * R/pMatrix.R: + setAs()  to dMatrix and from nMatrix
89            * man/pMatrix-class.Rd: ditto
90    
91            * R/Matrix.R (Summary): method for non-dMatrix
92    
93            * tests/Class+Meth.R (extraValid): new check about "dirty" slots
94            * tests/Class+Meth.R (tstMatrixClass): test norm(.);
95                    test all Summary methods.
96    
97    2007-07-16  Martin Maechler  <maechler@stat.math.ethz.ch>
98    
99            * R/dgeMatrix.R (norm, rcond): methods for 'matrix'
100    
101    2007-07-14  Martin Maechler  <maechler@stat.math.ethz.ch>
102    
103            * R/sparseMatrix.R (norm): simple methods for sparseMatrix
104    
105            * R/pMatrix.R (t?crossprod): methods for pMatrix
106    
107    2007-07-10  Douglas Bates  <bates@stat.wisc.edu>
108    
109            * src/dgeMatrix.c (dgeMatrix_colsums): Get the logic straight.
110    
111    2007-07-09 20:45  Douglas Bates <bates@stat.wisc.edu>
112    
113            * [r4579] src/dgeMatrix.c: Untangle horrible code in dgeMatrix_colsums
114              trying to fix a subtle bug - which has been somewhere else.
115    
116    2007-07-09 19:43  Martin Maechler <maechler@stat.math.ethz.ch>
117    
118            * [r4578] src/dgeMatrix.c: "cleaned" dgeMatrix_colsums() - but did not
119              solve the bug
120    
121    2007-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
122    
123            * src/dgCMatrix.c (compressed_to_TMatrix):
124    
125    2007-07-07  Martin Maechler  <maechler@stat.math.ethz.ch>
126    
127            * src/Csparse.c (Rsparse_validate): new, to have some validity
128            checking for RsparseMatrix
129            * src/dgCMatrix.c (xRMatrix_validate): ditto
130            * src/dtCMatrix.c (tRMatrix_validate): ditto
131    
132    2007-07-07  Douglas Bates <bates@stat.wisc.edu>
133    
134            * [r4567] R/AllClass.R: Slots already in RsparseMatrix were redefined in
135              lgRMatrix
136            * [r4568] DESCRIPTION: Prepare for bug-fix release
137            * [r4570] src/CHOLMOD/Check/cholmod_write.c: Include cholmod_matrixops.h
138              for declaration of cholmod_symmetry
139    
140    2007-07-06  Martin Maechler  <maechler@stat.math.ethz.ch>
141    
142            * DESCRIPTION (Version): 0.999375 merged into the trunk; ready for
143            release.
144    
145    2007-07-06 14:11  Douglas Bates <bates@stat.wisc.edu>
146    
147            * [r4559] src/iohb.c, src/iohb.h: Remove Harwell-Boeing input/output
148              functions - no longer used
149            * [r4560] src/HBMM.c, src/Mutils.c, src/dgTMatrix.c, src/dgeMatrix.c,
150              src/dspMatrix.c, src/dsyMatrix.c, src/dtCMatrix.c,
151              src/factorizations.c, src/sparseQR.c: Replace most calls to Calloc by
152              Alloca
153    
154    2007-07-06 13:14  Martin Maechler <maechler@stat.math.ethz.ch>
155    
156            * [r4558] inst/doc/Comparisons.Rnw, src/CHMfactor.c, src/Csparse.c,
157              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dense.c,
158              src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c, src/sparseQR.c,
159              src/t_gCMatrix_colSums.c: more R_CheckStack()s
160    
161    2007-07-05 18:12  Douglas Bates <bates@stat.wisc.edu>
162    
163            * [r4550] inst/include/Matrix.h: Add the macro N_AS_CHM_DN to "alloca"
164              the required amount of memory then call M_numeric_as_chm_dense.
165            * [r4556] src/Mutils.h, src/dgCMatrix.c: Define and use the Alloca macro
166              (like Calloc but calling alloca)
167    
168    2007-07-05  Martin Maechler  <maechler@stat.math.ethz.ch>
169    
170            * R/sparseMatrix.R (printSpMatrix): renamed from prSpMatrix()
171            and extended with more sophisticated 'col.names' option.
172            * NAMESPACE: export  printSparseMatrix()
173            * man/printSpMatrix.Rd: document, incl. examples
174    
175    2007-07-04 16:21  Douglas Bates <bates@stat.wisc.edu>
176    
177            * [r4543] src/cs_utils.c, src/cs_utils.h, src/dgCMatrix.c,
178              src/dtCMatrix.c, src/sparseQR.c: CSP typedef for *cs and macro
179              AS_CSP. API change - pass the empty structure to Matrix_as_cs.
180    
181    2007-07-04  Martin Maechler  <maechler@stat.math.ethz.ch>
182    
183            * DESCRIPTION (Version): 0.99875-4
184    
185            * tests/Class+Meth.R (tstMatrixClass): add dimnames, and hence test
186            some dimnames perservation.
187    
188            * R/dsTMatrix.R (t-method): keep dimnames
189            * R/dtTMatrix.R:  ditto
190    
191            * R/sparseMatrix.R (prSpMatrix): print colnames when non-trivial
192            and ncol(.) < 10
193    
194            * src/cs_utils.c: drop check_class() and use Matrix_check_class()
195            from Mutils.h
196    
197            * src/lgCMatrix.c ([ln]csc_to_matrix): no longer lose dimnames,
198            e.g. in as(<ngCMatrix>, "matrix")
199    
200    2007-07-01 13:27  Douglas Bates <bates@stat.wisc.edu>
201    
202            * [r4529] .: Create a branch for the API changes from the 0.99875
203              series to the 0.999375 series
204            * [r4530] DESCRIPTION, inst/include/Matrix.h,
205              inst/include/Matrix_stubs.c, src/CHMfactor.c, src/Csparse.c,
206              src/Mutils.h, src/Tsparse.c, src/chm_common.c, src/chm_common.h,
207              src/dense.c, src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c,
208              src/t_gCMatrix_colSums.c: API change - pass the empty structure to the
209              as_cholmod_x functions
210    
211    2007-06-30 09:05  Martin Maechler <maechler@stat.math.ethz.ch>
212    
213            * [r4527] trunk/Matrix/DESCRIPTION, trunk/Matrix/NAMESPACE,
214              trunk/Matrix/inst/doc/Comparisons.Rnw: add session- and hardware-info
215              to Comparisons
216    
217    >>>>>>> .merge-right.r4561
218    2007-06-29  Martin Maechler  <maechler@stat.math.ethz.ch>
219    
220            * DESCRIPTION (Version): 0.99875-3 ready to be released.
221    
222            * R/sparseMatrix.R (spMatrix): make spMatrix(3,4) working
223    
224            * R/AllGeneric.R: set "Math" (and "Math2") group generics in a way
225            that should also work in a future version of R.
226    
227    2007-06-21  Martin Maechler  <maechler@stat.math.ethz.ch>
228    
229            * NAMESPACE, R/AllClass.R: "xsparseVector" class union.
230    
231            * R/sparseVector.R: more *sparseVector coercions, notably for
232            non - double ones.
233    
234    2007-06-19  Martin Maechler  <maechler@stat.math.ethz.ch>
235    
236            * R/colSums.R: new file for all (col|row)(Sums|Means) methods,
237              notably the new ones building on the new .Call(.)s:
238    
239            * src/dgCMatrix.c (DEF_gCMatrix_COLSUMS): use to define
240            all 4 of [dlin]gCMatrix_colSums().
241    
242    2007-06-18 16:12  Douglas Bates <bates@stat.wisc.edu>
243    
244            * [r4472] src/Syms.h, src/init.c: Added Matrix_lengthSym
245            * [r4473] src/dgCMatrix.c: Modified dgCMatrix_colSums for sparseVector
246              result
247    
248    2007-06-16  Martin Maechler  <maechler@stat.math.ethz.ch>
249    
250            * R/kronecker.R: fix typo (could lead to inf.recursion)
251            * test/simple.R: testing that
252    
253            * R/sparseMatrix.R (prSpMatrix): change to be used as print()
254            method as well (which can have arguments, show() can't).
255    
256    2007-06-16 15:52  Douglas Bates <bates@stat.wisc.edu>
257    
258            * [r4466] R/dgCMatrix.R, src/dgCMatrix.c, src/dgCMatrix.h, src/init.c:
259              added dgCMatrix_colSums for [col,row][Sums,Means]
260    
261    2007-06-15 23:15  Douglas Bates <bates@stat.wisc.edu>
262    
263            * [r4460] R/sparseMatrix.R, man/dgCMatrix-class.Rd, src/dgCMatrix.c,
264              src/dgCMatrix.h, src/init.c: added lm.fit.sparse (unexported),
265              coercion of "factor" to "dgCMatrix" and dgCMatrix_cholsol
266            * [r4461] R/AllClass.R, man/sparseMatrix-class.Rd: draft "indicators"
267              class
268            * [r4463] R/sparseMatrix.R, man/dgCMatrix-class.Rd,
269              man/sparseMatrix-class.Rd: Don't need an "indicators" class - use the
270              row names to store the levels - duh!  Added an example.
271    
272    2007-06-14  Martin Maechler  <maechler@stat.math.ethz.ch>
273    
274            * src/Csparse.c (Csparse_validate): check for *repeated* entries
275            thanks to example from Christian Buchta; with a test here:
276            * tests/simple.R:
277    
278    2007-06-07  Martin Maechler  <maechler@stat.math.ethz.ch>
279    
280            * R/Auxiliaries.R (callGeneric): another fix, needed for some cases
281            of colSums(*, sparseResult = TRUE)
282    
283    2007-06-06  Martin Maechler  <maechler@stat.math.ethz.ch>
284    
285            * R/lsparseMatrix.R, R/ldenseMatrix.R (all, any): change default to
286            'na.rm = FALSE' as "everywhere" else in R.
287    
288    2007-06-05 Douglas Bates <bates@stat.wisc.edu>
289    
290            * [r4421] src/CSparse_install.sh: Modify for new organization of
291              CSparse package
292            * [r4425] src/UFsparse_download.sh: Update to version 3.0.0 of
293              SuiteSparse
294            * [r4426] src/Makefile: add ./UFconfig to the include path for
295              compilation
296            * [r4427] src/cs.[ch]: update to CSparse version 2.2.0
297            * [r4428] inst/doc/UFsparse/* src/{AMD,CHOLMOD,COLAMD}/*
298              src/UFconfig/UFconfig.h: Update to version 3.0.0 of SuiteSparse
299    
300    2007-06-05  Martin Maechler  <maechler@stat.math.ethz.ch>
301    
302            * R/Auxiliaries.R (emptyColnames): + argument msg.if.not.empty, used in
303            * R/sparseMatrix.R (prSpMatrix): now gives a message about
304            suppressed column names.
305    
306    2007-06-04 17:13  Douglas Bates <bates@stat.wisc.edu>
307    
308            * [r4418] src/Csparse.c, src/HBMM.c, src/Mutils.c, src/Mutils.h,
309              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dgCMatrix.c,
310              src/dgeMatrix.c, src/dpoMatrix.c, src/dpoMatrix.h, src/dppMatrix.c,
311              src/dppMatrix.h, src/dsCMatrix.c, src/dspMatrix.c, src/dspMatrix.h,
312              src/dsyMatrix.c, src/dsyMatrix.h, src/dtpMatrix.c, src/dtrMatrix.c:
313              Remove warnings after change to const char* CHAR
314    
315    2007-06-04 17:11  Douglas Bates <bates@stat.wisc.edu>
316    
317            * [r4417] inst/include/Matrix_stubs.c, inst/include/cholmod.h: Corrected
318              type of M_cholmod_ssmult
319    
320    2007-06-03 14:42  Douglas Bates <bates@stat.wisc.edu>
321    
322            * [r4412] inst/include/Matrix_stubs.c, inst/include/cholmod.h,
323              src/init.c: Yet another cholmod export - cholmod_ssmult
324    
325    2007-05-23  Martin Maechler  <maechler@stat.math.ethz.ch>
326    
327            * NAMESPACE: exported drop0(), since
328            * man/drop0.Rd: I have seen several cases, I really wanted to use
329            it, so our users may want too.
330    
331    2007-05-22  Martin Maechler  <maechler@stat.math.ethz.ch>
332    
333            * man/colSums.Rd: separately document colSums() etc, since these
334            have the extra argument 'sparseResult'.
335    
336    2007-05-21  Martin Maechler  <maechler@stat.math.ethz.ch>
337    
338            * R/sparseMatrix.R (spMatrix): utility (T)sparse Matrix constructor;
339            * man/spMatrix.Rd: docu., including examples
340    
341            * R/Auxiliaries.R (sp.colMeans): etc, using a patched callGeneric(),
342            in order to make colMeans() etc fast *and* correct.
343            * R/sparseVector.R (replSPvec): "[<-" functionality for
344            sparseVectors; tested in
345            * tests/simple.R:
346    
347    2007-05-19  Martin Maechler  <maechler@stat.math.ethz.ch>
348    
349            * R/sparseMatrix.R (print.sparseSummary): and summary() method for
350            (very) sparse Matrices; output similar to Matlab's print().
351    
352    2007-05-17  Douglas Bates  <bates@stat.wisc.edu>
353    
354            * src/HBMM.c (Matrix_writeMatrixMarket): Write 1-based, not
355            0-based, indices (Jose Quesada <quesada@gmail.com>).
356    
357    2007-05-16  Douglas Bates  <bates@stat.wisc.edu>
358    
359            * R/CHMfactor.R: Added solve methods for a CHMfactor object.
360    
361    2007-05-16  Martin Maechler  <maechler@stat.math.ethz.ch>
362    
363            * R/Auxiliaries.R (sparsapply): new utility, much faster than
364            tapply1() for large sparse matrices.
365    
366    2007-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
367    
368            * R/Matrix.R (dim<-): reshape now via sparseVector.
369    
370            * R/sparseVector.R: methods and function for
371            * R/AllClass.R: new "sparseVector" class and daughters.
372            * NAMESPACE: export new classes
373    
374    2007-05-14  Martin Maechler  <maechler@stat.math.ethz.ch>
375    
376            * DESCRIPTION (Version): 0.99875-1
377            * src/Makefile.win: also remove Lapack code from here (cf. 04-25).
378    
379    2007-05-11  Martin Maechler  <maechler@stat.math.ethz.ch>
380    
381            * R/Tsparse.R ([, Tsparse): fix last case: *duplicated*, symmetric
382            indexing
383            * tests/indexing.R: test set for that.
384    
385    2007-05-08  Martin Maechler  <maechler@stat.math.ethz.ch>
386    
387            * R/Tsparse.R (replTmat): fix the case of *duplicated* index
388            entries.
389            * tests/indexing.R(out): add regression test for it
390    
391    2007-04-30  Martin Maechler  <maechler@stat.math.ethz.ch>
392    
393            * R/(l(dense|sparse))?Matrix.R (!): use 'x', not 'e1' as argument
394            name for "!" method definitions.
395    
396    2007-04-26  Martin Maechler  <maechler@stat.math.ethz.ch>
397    
398            * R/Tsparse.R (intI): new utility, used for "[" :
399                    Cleanup up there, and fixes for duplicated indices - more TODO!
400    
401            * tests/indexing.R(out): more tests
402    
403  2007-04-25  Douglas Bates  <bates@stat.wisc.edu>  2007-04-25  Douglas Bates  <bates@stat.wisc.edu>
404    
405          * DESCRIPTION,src/Makefile: require R>= 2.5.0 and remove Lapack          * DESCRIPTION,src/Makefile: require R>= 2.5.0 and remove Lapack
# Line 6  Line 408 
408          * src/init.c,inst/include/{Matrix_stubs.c,cholmod.h}:export          * src/init.c,inst/include/{Matrix_stubs.c,cholmod.h}:export
409          cholmod_factorize_p (used in lme4 for GLMMs and NLMMs).          cholmod_factorize_p (used in lme4 for GLMMs and NLMMs).
410    
411    2007-04-21  Martin Maechler  <maechler@stat.math.ethz.ch>
412    
413            * R/Matrix.R (image): method for all Matrices, not just sparse ones.
414    
415    2007-04-17  Martin Maechler  <maechler@stat.math.ethz.ch>
416    
417            * R/Auxiliaries.R (tapply1): unname(.) -> colSums() etc don't end
418            up with extraneous names '0'...'<n-1>'
419    
420  2007-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>  2007-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
421    
422          * R/dgTMatrix.R (mat2dgT): care about NAs          * R/dgTMatrix.R (mat2dgT): care about NAs

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