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revision 1852, Mon May 21 16:42:35 2007 UTC revision 2041, Tue Aug 7 11:09:11 2007 UTC
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1    2007-08-06  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * src/dsyMatrix.c (dsyMatrix_matrix_mm): 'b' might be matrix;
4            must copy its *expanded* x slot before LAPACK call.
5    
6            * tests/matprod.R: test the last days' changes.
7    
8    2007-08-06 16:43  Douglas Bates <bates@stat.wisc.edu>
9    
10            * [r4712] inst/include/Matrix_stubs.c: Change R_cholmod_printf in stubs
11              as well as in sources
12    
13    2007-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
14    
15            * R/Matrix.R (%*%, crossprod, tcrossprod): add method for
16                    ("Matrix", "matrix") which is needed in some cases.
17            Ditto for solve().
18    
19            * R/colSums.R (.as.dge.Fun): need ddenseMatrix methods to avoid
20            infinite recursion in dispatch for some cases.
21    
22    2007-08-02 08:48  Martin Maechler <maechler@stat.math.ethz.ch>
23    
24            * [r4693] src/chm_common.c: R_cholmod_printf() instead of Rprintf() just
25              so pointers match
26    
27    2007-08-02  Martin Maechler  <maechler@stat.math.ethz.ch>
28    
29            * DESCRIPTION (Date): set ready for release -- 0.999375-1
30    
31    2007-08-01 15:44  Douglas Bates <bates@stat.wisc.edu>
32    
33            * [r4686] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
34              src/chm_common.c, src/chm_common.h: Change API for
35              numeric_as_chm_dense and N_AS_CHM_DN
36    
37    2007-08-01  Martin Maechler  <maechler@stat.math.ethz.ch>
38    
39            * src/dtrMatrix.c (dtrMatrix_matrix_mm): fix dimensionality check (!)
40            * tests/matprod.R: regr.test for it
41    
42    2007-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
43    
44            * R/dMatrix.R: fix from Brian for   Math2(., digits = "missing")
45            * tests/group-methods.R: and regression-test it
46    
47    2007-07-19 19:45  Douglas Bates <bates@stat.wisc.edu>
48    
49            * [r4642] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
50              inst/include/cholmod.h, src/chm_common.c, src/init.c: Export
51              triplet_to_sparse, documentation, use typedefs
52    
53    2007-07-18  Martin Maechler  <maechler@stat.math.ethz.ch>
54    
55            * man/dpoMatrix-class.Rd: added 'corMatrix' example
56    
57            * src/dsyMatrix.[ch] (dsyMatrix_as_matrix): new 'keep_dimnames' arg
58            * src/dtrMatrix.[ch] (dtrMatrix_as_matrix): ditto
59            * src/init.c, R/dsyMatrix.R, R/dtrMatrix.R, R/lgTMatrix.R: ditto
60    
61            * R/lsparseMatrix.R: bug fix in "all" method
62            * R/Ops.R (.do.Logic.lsparse): "|" bug in borderline case
63    
64            * R/dsyMatrix.R (coerce->dsTMatrix): (i,j) slots should *not* have names
65            * R/ngTMatrix.R (coerce->ngTMatrix): ditto;
66                    + matrix |-> nMatrix coercion
67            * R/pMatrix.R: + setAs()  to dMatrix and from nMatrix
68            * man/pMatrix-class.Rd: ditto
69    
70            * R/Matrix.R (Summary): method for non-dMatrix
71    
72            * tests/Class+Meth.R (extraValid): new check about "dirty" slots
73            * tests/Class+Meth.R (tstMatrixClass): test norm(.);
74                    test all Summary methods.
75    
76    2007-07-16  Martin Maechler  <maechler@stat.math.ethz.ch>
77    
78            * R/dgeMatrix.R (norm, rcond): methods for 'matrix'
79    
80    2007-07-14  Martin Maechler  <maechler@stat.math.ethz.ch>
81    
82            * R/sparseMatrix.R (norm): simple methods for sparseMatrix
83    
84            * R/pMatrix.R (t?crossprod): methods for pMatrix
85    
86    2007-07-10  Douglas Bates  <bates@stat.wisc.edu>
87    
88            * src/dgeMatrix.c (dgeMatrix_colsums): Get the logic straight.
89    
90    2007-07-09 20:45  Douglas Bates <bates@stat.wisc.edu>
91    
92            * [r4579] src/dgeMatrix.c: Untangle horrible code in dgeMatrix_colsums
93              trying to fix a subtle bug - which has been somewhere else.
94    
95    2007-07-09 19:43  Martin Maechler <maechler@stat.math.ethz.ch>
96    
97            * [r4578] src/dgeMatrix.c: "cleaned" dgeMatrix_colsums() - but did not
98              solve the bug
99    
100    2007-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
101    
102            * src/dgCMatrix.c (compressed_to_TMatrix):
103    
104    2007-07-07  Martin Maechler  <maechler@stat.math.ethz.ch>
105    
106            * src/Csparse.c (Rsparse_validate): new, to have some validity
107            checking for RsparseMatrix
108            * src/dgCMatrix.c (xRMatrix_validate): ditto
109            * src/dtCMatrix.c (tRMatrix_validate): ditto
110    
111    2007-07-07  Douglas Bates <bates@stat.wisc.edu>
112    
113            * [r4567] R/AllClass.R: Slots already in RsparseMatrix were redefined in
114              lgRMatrix
115            * [r4568] DESCRIPTION: Prepare for bug-fix release
116            * [r4570] src/CHOLMOD/Check/cholmod_write.c: Include cholmod_matrixops.h
117              for declaration of cholmod_symmetry
118    
119    2007-07-06  Martin Maechler  <maechler@stat.math.ethz.ch>
120    
121            * DESCRIPTION (Version): 0.999375 merged into the trunk; ready for
122            release.
123    
124    2007-07-06 14:11  Douglas Bates <bates@stat.wisc.edu>
125    
126            * [r4559] src/iohb.c, src/iohb.h: Remove Harwell-Boeing input/output
127              functions - no longer used
128            * [r4560] src/HBMM.c, src/Mutils.c, src/dgTMatrix.c, src/dgeMatrix.c,
129              src/dspMatrix.c, src/dsyMatrix.c, src/dtCMatrix.c,
130              src/factorizations.c, src/sparseQR.c: Replace most calls to Calloc by
131              Alloca
132    
133    2007-07-06 13:14  Martin Maechler <maechler@stat.math.ethz.ch>
134    
135            * [r4558] inst/doc/Comparisons.Rnw, src/CHMfactor.c, src/Csparse.c,
136              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dense.c,
137              src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c, src/sparseQR.c,
138              src/t_gCMatrix_colSums.c: more R_CheckStack()s
139    
140    2007-07-05 18:12  Douglas Bates <bates@stat.wisc.edu>
141    
142            * [r4550] inst/include/Matrix.h: Add the macro N_AS_CHM_DN to "alloca"
143              the required amount of memory then call M_numeric_as_chm_dense.
144            * [r4556] src/Mutils.h, src/dgCMatrix.c: Define and use the Alloca macro
145              (like Calloc but calling alloca)
146    
147    2007-07-05  Martin Maechler  <maechler@stat.math.ethz.ch>
148    
149            * R/sparseMatrix.R (printSpMatrix): renamed from prSpMatrix()
150            and extended with more sophisticated 'col.names' option.
151            * NAMESPACE: export  printSparseMatrix()
152            * man/printSpMatrix.Rd: document, incl. examples
153    
154    2007-07-04 16:21  Douglas Bates <bates@stat.wisc.edu>
155    
156            * [r4543] src/cs_utils.c, src/cs_utils.h, src/dgCMatrix.c,
157              src/dtCMatrix.c, src/sparseQR.c: CSP typedef for *cs and macro
158              AS_CSP. API change - pass the empty structure to Matrix_as_cs.
159    
160    2007-07-04  Martin Maechler  <maechler@stat.math.ethz.ch>
161    
162            * DESCRIPTION (Version): 0.99875-4
163    
164            * tests/Class+Meth.R (tstMatrixClass): add dimnames, and hence test
165            some dimnames perservation.
166    
167            * R/dsTMatrix.R (t-method): keep dimnames
168            * R/dtTMatrix.R:  ditto
169    
170            * R/sparseMatrix.R (prSpMatrix): print colnames when non-trivial
171            and ncol(.) < 10
172    
173            * src/cs_utils.c: drop check_class() and use Matrix_check_class()
174            from Mutils.h
175    
176            * src/lgCMatrix.c ([ln]csc_to_matrix): no longer lose dimnames,
177            e.g. in as(<ngCMatrix>, "matrix")
178    
179    2007-07-01 13:27  Douglas Bates <bates@stat.wisc.edu>
180    
181            * [r4529] .: Create a branch for the API changes from the 0.99875
182              series to the 0.999375 series
183            * [r4530] DESCRIPTION, inst/include/Matrix.h,
184              inst/include/Matrix_stubs.c, src/CHMfactor.c, src/Csparse.c,
185              src/Mutils.h, src/Tsparse.c, src/chm_common.c, src/chm_common.h,
186              src/dense.c, src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c,
187              src/t_gCMatrix_colSums.c: API change - pass the empty structure to the
188              as_cholmod_x functions
189    
190    2007-06-30 09:05  Martin Maechler <maechler@stat.math.ethz.ch>
191    
192            * [r4527] trunk/Matrix/DESCRIPTION, trunk/Matrix/NAMESPACE,
193              trunk/Matrix/inst/doc/Comparisons.Rnw: add session- and hardware-info
194              to Comparisons
195    
196    >>>>>>> .merge-right.r4561
197    2007-06-29  Martin Maechler  <maechler@stat.math.ethz.ch>
198    
199            * DESCRIPTION (Version): 0.99875-3 ready to be released.
200    
201            * R/sparseMatrix.R (spMatrix): make spMatrix(3,4) working
202    
203            * R/AllGeneric.R: set "Math" (and "Math2") group generics in a way
204            that should also work in a future version of R.
205    
206    2007-06-21  Martin Maechler  <maechler@stat.math.ethz.ch>
207    
208            * NAMESPACE, R/AllClass.R: "xsparseVector" class union.
209    
210            * R/sparseVector.R: more *sparseVector coercions, notably for
211            non - double ones.
212    
213    2007-06-19  Martin Maechler  <maechler@stat.math.ethz.ch>
214    
215            * R/colSums.R: new file for all (col|row)(Sums|Means) methods,
216              notably the new ones building on the new .Call(.)s:
217    
218            * src/dgCMatrix.c (DEF_gCMatrix_COLSUMS): use to define
219            all 4 of [dlin]gCMatrix_colSums().
220    
221    2007-06-18 16:12  Douglas Bates <bates@stat.wisc.edu>
222    
223            * [r4472] src/Syms.h, src/init.c: Added Matrix_lengthSym
224            * [r4473] src/dgCMatrix.c: Modified dgCMatrix_colSums for sparseVector
225              result
226    
227    2007-06-16  Martin Maechler  <maechler@stat.math.ethz.ch>
228    
229            * R/kronecker.R: fix typo (could lead to inf.recursion)
230            * test/simple.R: testing that
231    
232            * R/sparseMatrix.R (prSpMatrix): change to be used as print()
233            method as well (which can have arguments, show() can't).
234    
235    2007-06-16 15:52  Douglas Bates <bates@stat.wisc.edu>
236    
237            * [r4466] R/dgCMatrix.R, src/dgCMatrix.c, src/dgCMatrix.h, src/init.c:
238              added dgCMatrix_colSums for [col,row][Sums,Means]
239    
240    2007-06-15 23:15  Douglas Bates <bates@stat.wisc.edu>
241    
242            * [r4460] R/sparseMatrix.R, man/dgCMatrix-class.Rd, src/dgCMatrix.c,
243              src/dgCMatrix.h, src/init.c: added lm.fit.sparse (unexported),
244              coercion of "factor" to "dgCMatrix" and dgCMatrix_cholsol
245            * [r4461] R/AllClass.R, man/sparseMatrix-class.Rd: draft "indicators"
246              class
247            * [r4463] R/sparseMatrix.R, man/dgCMatrix-class.Rd,
248              man/sparseMatrix-class.Rd: Don't need an "indicators" class - use the
249              row names to store the levels - duh!  Added an example.
250    
251    2007-06-14  Martin Maechler  <maechler@stat.math.ethz.ch>
252    
253            * src/Csparse.c (Csparse_validate): check for *repeated* entries
254            thanks to example from Christian Buchta; with a test here:
255            * tests/simple.R:
256    
257    2007-06-07  Martin Maechler  <maechler@stat.math.ethz.ch>
258    
259            * R/Auxiliaries.R (callGeneric): another fix, needed for some cases
260            of colSums(*, sparseResult = TRUE)
261    
262    2007-06-06  Martin Maechler  <maechler@stat.math.ethz.ch>
263    
264            * R/lsparseMatrix.R, R/ldenseMatrix.R (all, any): change default to
265            'na.rm = FALSE' as "everywhere" else in R.
266    
267    2007-06-05 Douglas Bates <bates@stat.wisc.edu>
268    
269            * [r4421] src/CSparse_install.sh: Modify for new organization of
270              CSparse package
271            * [r4425] src/UFsparse_download.sh: Update to version 3.0.0 of
272              SuiteSparse
273            * [r4426] src/Makefile: add ./UFconfig to the include path for
274              compilation
275            * [r4427] src/cs.[ch]: update to CSparse version 2.2.0
276            * [r4428] inst/doc/UFsparse/* src/{AMD,CHOLMOD,COLAMD}/*
277              src/UFconfig/UFconfig.h: Update to version 3.0.0 of SuiteSparse
278    
279    2007-06-05  Martin Maechler  <maechler@stat.math.ethz.ch>
280    
281            * R/Auxiliaries.R (emptyColnames): + argument msg.if.not.empty, used in
282            * R/sparseMatrix.R (prSpMatrix): now gives a message about
283            suppressed column names.
284    
285    2007-06-04 17:13  Douglas Bates <bates@stat.wisc.edu>
286    
287            * [r4418] src/Csparse.c, src/HBMM.c, src/Mutils.c, src/Mutils.h,
288              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dgCMatrix.c,
289              src/dgeMatrix.c, src/dpoMatrix.c, src/dpoMatrix.h, src/dppMatrix.c,
290              src/dppMatrix.h, src/dsCMatrix.c, src/dspMatrix.c, src/dspMatrix.h,
291              src/dsyMatrix.c, src/dsyMatrix.h, src/dtpMatrix.c, src/dtrMatrix.c:
292              Remove warnings after change to const char* CHAR
293    
294    2007-06-04 17:11  Douglas Bates <bates@stat.wisc.edu>
295    
296            * [r4417] inst/include/Matrix_stubs.c, inst/include/cholmod.h: Corrected
297              type of M_cholmod_ssmult
298    
299    2007-06-03 14:42  Douglas Bates <bates@stat.wisc.edu>
300    
301            * [r4412] inst/include/Matrix_stubs.c, inst/include/cholmod.h,
302              src/init.c: Yet another cholmod export - cholmod_ssmult
303    
304    2007-05-23  Martin Maechler  <maechler@stat.math.ethz.ch>
305    
306            * NAMESPACE: exported drop0(), since
307            * man/drop0.Rd: I have seen several cases, I really wanted to use
308            it, so our users may want too.
309    
310    2007-05-22  Martin Maechler  <maechler@stat.math.ethz.ch>
311    
312            * man/colSums.Rd: separately document colSums() etc, since these
313            have the extra argument 'sparseResult'.
314    
315  2007-05-21  Martin Maechler  <maechler@stat.math.ethz.ch>  2007-05-21  Martin Maechler  <maechler@stat.math.ethz.ch>
316    
317          * R/sparseMatrix.R (spMatrix): utility (T)sparse Matrix constructor;          * R/sparseMatrix.R (spMatrix): utility (T)sparse Matrix constructor;

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