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revision 1870, Tue Jun 5 16:28:55 2007 UTC revision 2050, Tue Aug 14 22:23:33 2007 UTC
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1    2007-08-14 13:07  Douglas Bates <bates@stat.wisc.edu>
2    
3            * [r4730] src/Mutils.h: declare alloca
4            * [r4734] NAMESPACE, R/AllGeneric.R, R/Csparse.R, R/HBMM.R, R/Tsparse.R,
5              R/dgCMatrix.R, R/dgTMatrix.R, R/dsCMatrix.R, R/dsTMatrix.R,
6              man/externalFormats.Rd, src/Csparse.c, src/Csparse.h, src/DEPS.mkf,
7              src/HBMM.c, src/HBMM.h, src/Mutils.h, src/SOURCES_C.mkf, src/init.c,
8              src/mmio.c, src/mmio.h: Remove deprecated function writeHB and its
9              methods; switch writeMM to use CHOLMOD code; repair readMM
10    
11    
12    2007-08-14  Martin Maechler  <maechler@stat.math.ethz.ch>
13    
14            * R/nearPD.R, man/nearPD.Rd (nearPD): new function built on Jens
15            Oehlschlaegel's ... result type still to be discussed!
16    
17    2007-08-10  Martin Maechler  <maechler@stat.math.ethz.ch>
18    
19            * man/image-methods.Rd: new, combining all image() methods
20    
21    2007-08-09  Martin Maechler  <maechler@stat.math.ethz.ch>
22    
23            * R/dgCMatrix.R: define qr() and lu() methods for "sparseMatrix"
24            to work via dgC...
25    
26            * R/Matrix.R (Matrix): special treatment for "table" (S3)
27    
28    2007-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
29    
30            * R/dgTMatrix.R (image): change defaults to
31                    aspect = "iso", colorkey = FALSE
32    
33    2007-08-06  Martin Maechler  <maechler@stat.math.ethz.ch>
34    
35            * src/dsyMatrix.c (dsyMatrix_matrix_mm): 'b' might be matrix;
36            must copy its *expanded* x slot before LAPACK call.
37    
38            * tests/matprod.R: test the last days' changes.
39    
40    2007-08-06 16:43  Douglas Bates <bates@stat.wisc.edu>
41    
42            * [r4712] inst/include/Matrix_stubs.c: Change R_cholmod_printf in stubs
43              as well as in sources
44            * [r4713] src/dsyMatrix.c: Duplicate the contents of the RHS before
45              Lapack call
46    
47    2007-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
48    
49            * R/Matrix.R (%*%, crossprod, tcrossprod): add method for
50                    ("Matrix", "matrix") which is needed in some cases.
51            Ditto for solve().
52    
53            * R/colSums.R (.as.dge.Fun): need ddenseMatrix methods to avoid
54            infinite recursion in dispatch for some cases.
55    
56    2007-08-02 08:48  Martin Maechler <maechler@stat.math.ethz.ch>
57    
58            * [r4693] src/chm_common.c: R_cholmod_printf() instead of Rprintf() just
59              so pointers match
60    
61    2007-08-02  Martin Maechler  <maechler@stat.math.ethz.ch>
62    
63            * DESCRIPTION (Date): set ready for release -- 0.999375-1
64    
65    2007-08-01 15:44  Douglas Bates <bates@stat.wisc.edu>
66    
67            * [r4686] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
68              src/chm_common.c, src/chm_common.h: Change API for
69              numeric_as_chm_dense and N_AS_CHM_DN
70    
71    2007-08-01  Martin Maechler  <maechler@stat.math.ethz.ch>
72    
73            * src/dtrMatrix.c (dtrMatrix_matrix_mm): fix dimensionality check (!)
74            * tests/matprod.R: regr.test for it
75    
76    2007-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
77    
78            * R/dMatrix.R: fix from Brian for   Math2(., digits = "missing")
79            * tests/group-methods.R: and regression-test it
80    
81    2007-07-19 19:45  Douglas Bates <bates@stat.wisc.edu>
82    
83            * [r4642] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
84              inst/include/cholmod.h, src/chm_common.c, src/init.c: Export
85              triplet_to_sparse, documentation, use typedefs
86    
87    2007-07-18  Martin Maechler  <maechler@stat.math.ethz.ch>
88    
89            * man/dpoMatrix-class.Rd: added 'corMatrix' example
90    
91            * src/dsyMatrix.[ch] (dsyMatrix_as_matrix): new 'keep_dimnames' arg
92            * src/dtrMatrix.[ch] (dtrMatrix_as_matrix): ditto
93            * src/init.c, R/dsyMatrix.R, R/dtrMatrix.R, R/lgTMatrix.R: ditto
94    
95            * R/lsparseMatrix.R: bug fix in "all" method
96            * R/Ops.R (.do.Logic.lsparse): "|" bug in borderline case
97    
98            * R/dsyMatrix.R (coerce->dsTMatrix): (i,j) slots should *not* have names
99            * R/ngTMatrix.R (coerce->ngTMatrix): ditto;
100                    + matrix |-> nMatrix coercion
101            * R/pMatrix.R: + setAs()  to dMatrix and from nMatrix
102            * man/pMatrix-class.Rd: ditto
103    
104            * R/Matrix.R (Summary): method for non-dMatrix
105    
106            * tests/Class+Meth.R (extraValid): new check about "dirty" slots
107            * tests/Class+Meth.R (tstMatrixClass): test norm(.);
108                    test all Summary methods.
109    
110    2007-07-16  Martin Maechler  <maechler@stat.math.ethz.ch>
111    
112            * R/dgeMatrix.R (norm, rcond): methods for 'matrix'
113    
114    2007-07-14  Martin Maechler  <maechler@stat.math.ethz.ch>
115    
116            * R/sparseMatrix.R (norm): simple methods for sparseMatrix
117    
118            * R/pMatrix.R (t?crossprod): methods for pMatrix
119    
120    2007-07-10  Douglas Bates  <bates@stat.wisc.edu>
121    
122            * src/dgeMatrix.c (dgeMatrix_colsums): Get the logic straight.
123    
124    2007-07-09 20:45  Douglas Bates <bates@stat.wisc.edu>
125    
126            * [r4579] src/dgeMatrix.c: Untangle horrible code in dgeMatrix_colsums
127              trying to fix a subtle bug - which has been somewhere else.
128    
129    2007-07-09 19:43  Martin Maechler <maechler@stat.math.ethz.ch>
130    
131            * [r4578] src/dgeMatrix.c: "cleaned" dgeMatrix_colsums() - but did not
132              solve the bug
133    
134    2007-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
135    
136            * src/dgCMatrix.c (compressed_to_TMatrix):
137    
138    2007-07-07  Martin Maechler  <maechler@stat.math.ethz.ch>
139    
140            * src/Csparse.c (Rsparse_validate): new, to have some validity
141            checking for RsparseMatrix
142            * src/dgCMatrix.c (xRMatrix_validate): ditto
143            * src/dtCMatrix.c (tRMatrix_validate): ditto
144    
145    2007-07-07  Douglas Bates <bates@stat.wisc.edu>
146    
147            * [r4567] R/AllClass.R: Slots already in RsparseMatrix were redefined in
148              lgRMatrix
149            * [r4568] DESCRIPTION: Prepare for bug-fix release
150            * [r4570] src/CHOLMOD/Check/cholmod_write.c: Include cholmod_matrixops.h
151              for declaration of cholmod_symmetry
152    
153    2007-07-06  Martin Maechler  <maechler@stat.math.ethz.ch>
154    
155            * DESCRIPTION (Version): 0.999375 merged into the trunk; ready for
156            release.
157    
158    2007-07-06 14:11  Douglas Bates <bates@stat.wisc.edu>
159    
160            * [r4559] src/iohb.c, src/iohb.h: Remove Harwell-Boeing input/output
161              functions - no longer used
162            * [r4560] src/HBMM.c, src/Mutils.c, src/dgTMatrix.c, src/dgeMatrix.c,
163              src/dspMatrix.c, src/dsyMatrix.c, src/dtCMatrix.c,
164              src/factorizations.c, src/sparseQR.c: Replace most calls to Calloc by
165              Alloca
166    
167    2007-07-06 13:14  Martin Maechler <maechler@stat.math.ethz.ch>
168    
169            * [r4558] inst/doc/Comparisons.Rnw, src/CHMfactor.c, src/Csparse.c,
170              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dense.c,
171              src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c, src/sparseQR.c,
172              src/t_gCMatrix_colSums.c: more R_CheckStack()s
173    
174    2007-07-05 18:12  Douglas Bates <bates@stat.wisc.edu>
175    
176            * [r4550] inst/include/Matrix.h: Add the macro N_AS_CHM_DN to "alloca"
177              the required amount of memory then call M_numeric_as_chm_dense.
178            * [r4556] src/Mutils.h, src/dgCMatrix.c: Define and use the Alloca macro
179              (like Calloc but calling alloca)
180    
181    2007-07-05  Martin Maechler  <maechler@stat.math.ethz.ch>
182    
183            * R/sparseMatrix.R (printSpMatrix): renamed from prSpMatrix()
184            and extended with more sophisticated 'col.names' option.
185            * NAMESPACE: export  printSparseMatrix()
186            * man/printSpMatrix.Rd: document, incl. examples
187    
188    2007-07-04 16:21  Douglas Bates <bates@stat.wisc.edu>
189    
190            * [r4543] src/cs_utils.c, src/cs_utils.h, src/dgCMatrix.c,
191              src/dtCMatrix.c, src/sparseQR.c: CSP typedef for *cs and macro
192              AS_CSP. API change - pass the empty structure to Matrix_as_cs.
193    
194    2007-07-04  Martin Maechler  <maechler@stat.math.ethz.ch>
195    
196            * DESCRIPTION (Version): 0.99875-4
197    
198            * tests/Class+Meth.R (tstMatrixClass): add dimnames, and hence test
199            some dimnames perservation.
200    
201            * R/dsTMatrix.R (t-method): keep dimnames
202            * R/dtTMatrix.R:  ditto
203    
204            * R/sparseMatrix.R (prSpMatrix): print colnames when non-trivial
205            and ncol(.) < 10
206    
207            * src/cs_utils.c: drop check_class() and use Matrix_check_class()
208            from Mutils.h
209    
210            * src/lgCMatrix.c ([ln]csc_to_matrix): no longer lose dimnames,
211            e.g. in as(<ngCMatrix>, "matrix")
212    
213    2007-07-01 13:27  Douglas Bates <bates@stat.wisc.edu>
214    
215            * [r4529] .: Create a branch for the API changes from the 0.99875
216              series to the 0.999375 series
217            * [r4530] DESCRIPTION, inst/include/Matrix.h,
218              inst/include/Matrix_stubs.c, src/CHMfactor.c, src/Csparse.c,
219              src/Mutils.h, src/Tsparse.c, src/chm_common.c, src/chm_common.h,
220              src/dense.c, src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c,
221              src/t_gCMatrix_colSums.c: API change - pass the empty structure to the
222              as_cholmod_x functions
223    
224    2007-06-30 09:05  Martin Maechler <maechler@stat.math.ethz.ch>
225    
226            * [r4527] trunk/Matrix/DESCRIPTION, trunk/Matrix/NAMESPACE,
227              trunk/Matrix/inst/doc/Comparisons.Rnw: add session- and hardware-info
228              to Comparisons
229    
230    >>>>>>> .merge-right.r4561
231    2007-06-29  Martin Maechler  <maechler@stat.math.ethz.ch>
232    
233            * DESCRIPTION (Version): 0.99875-3 ready to be released.
234    
235            * R/sparseMatrix.R (spMatrix): make spMatrix(3,4) working
236    
237            * R/AllGeneric.R: set "Math" (and "Math2") group generics in a way
238            that should also work in a future version of R.
239    
240    2007-06-21  Martin Maechler  <maechler@stat.math.ethz.ch>
241    
242            * NAMESPACE, R/AllClass.R: "xsparseVector" class union.
243    
244            * R/sparseVector.R: more *sparseVector coercions, notably for
245            non - double ones.
246    
247    2007-06-19  Martin Maechler  <maechler@stat.math.ethz.ch>
248    
249            * R/colSums.R: new file for all (col|row)(Sums|Means) methods,
250              notably the new ones building on the new .Call(.)s:
251    
252            * src/dgCMatrix.c (DEF_gCMatrix_COLSUMS): use to define
253            all 4 of [dlin]gCMatrix_colSums().
254    
255    2007-06-18 16:12  Douglas Bates <bates@stat.wisc.edu>
256    
257            * [r4472] src/Syms.h, src/init.c: Added Matrix_lengthSym
258            * [r4473] src/dgCMatrix.c: Modified dgCMatrix_colSums for sparseVector
259              result
260    
261    2007-06-16  Martin Maechler  <maechler@stat.math.ethz.ch>
262    
263            * R/kronecker.R: fix typo (could lead to inf.recursion)
264            * test/simple.R: testing that
265    
266            * R/sparseMatrix.R (prSpMatrix): change to be used as print()
267            method as well (which can have arguments, show() can't).
268    
269    2007-06-16 15:52  Douglas Bates <bates@stat.wisc.edu>
270    
271            * [r4466] R/dgCMatrix.R, src/dgCMatrix.c, src/dgCMatrix.h, src/init.c:
272              added dgCMatrix_colSums for [col,row][Sums,Means]
273    
274    2007-06-15 23:15  Douglas Bates <bates@stat.wisc.edu>
275    
276            * [r4460] R/sparseMatrix.R, man/dgCMatrix-class.Rd, src/dgCMatrix.c,
277              src/dgCMatrix.h, src/init.c: added lm.fit.sparse (unexported),
278              coercion of "factor" to "dgCMatrix" and dgCMatrix_cholsol
279            * [r4461] R/AllClass.R, man/sparseMatrix-class.Rd: draft "indicators"
280              class
281            * [r4463] R/sparseMatrix.R, man/dgCMatrix-class.Rd,
282              man/sparseMatrix-class.Rd: Don't need an "indicators" class - use the
283              row names to store the levels - duh!  Added an example.
284    
285    2007-06-14  Martin Maechler  <maechler@stat.math.ethz.ch>
286    
287            * src/Csparse.c (Csparse_validate): check for *repeated* entries
288            thanks to example from Christian Buchta; with a test here:
289            * tests/simple.R:
290    
291    2007-06-07  Martin Maechler  <maechler@stat.math.ethz.ch>
292    
293            * R/Auxiliaries.R (callGeneric): another fix, needed for some cases
294            of colSums(*, sparseResult = TRUE)
295    
296    2007-06-06  Martin Maechler  <maechler@stat.math.ethz.ch>
297    
298            * R/lsparseMatrix.R, R/ldenseMatrix.R (all, any): change default to
299            'na.rm = FALSE' as "everywhere" else in R.
300    
301    2007-06-05 Douglas Bates <bates@stat.wisc.edu>
302    
303            * [r4421] src/CSparse_install.sh: Modify for new organization of
304              CSparse package
305            * [r4425] src/UFsparse_download.sh: Update to version 3.0.0 of
306              SuiteSparse
307            * [r4426] src/Makefile: add ./UFconfig to the include path for
308              compilation
309            * [r4427] src/cs.[ch]: update to CSparse version 2.2.0
310            * [r4428] inst/doc/UFsparse/* src/{AMD,CHOLMOD,COLAMD}/*
311              src/UFconfig/UFconfig.h: Update to version 3.0.0 of SuiteSparse
312    
313  2007-06-05  Martin Maechler  <maechler@stat.math.ethz.ch>  2007-06-05  Martin Maechler  <maechler@stat.math.ethz.ch>
314    
315          * R/Auxiliaries.R (emptyColnames): + argument msg.if.not.empty, used in          * R/Auxiliaries.R (emptyColnames): + argument msg.if.not.empty, used in

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