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revision 1877, Tue Jun 5 17:06:34 2007 UTC revision 2056, Thu Aug 16 16:42:10 2007 UTC
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1    2007-08-16  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * DESCRIPTION (Date, Version): 0.999375-2
4    
5    2007-08-15  Martin Maechler  <maechler@stat.math.ethz.ch>
6    
7            * R/HBMM.R (readMM): make work for pattern matrices as well
8    
9    2007-08-14 13:07  Douglas Bates <bates@stat.wisc.edu>
10    
11            * [r4730] src/Mutils.h: declare alloca
12            * [r4734] NAMESPACE, R/AllGeneric.R, R/Csparse.R, R/HBMM.R, R/Tsparse.R,
13              R/dgCMatrix.R, R/dgTMatrix.R, R/dsCMatrix.R, R/dsTMatrix.R,
14              man/externalFormats.Rd, src/Csparse.c, src/Csparse.h, src/DEPS.mkf,
15              src/HBMM.c, src/HBMM.h, src/Mutils.h, src/SOURCES_C.mkf, src/init.c,
16              src/mmio.c, src/mmio.h: Remove deprecated function writeHB and its
17              methods; switch writeMM to use CHOLMOD code; repair readMM
18    
19    2007-08-14  Martin Maechler  <maechler@stat.math.ethz.ch>
20    
21            * R/nearPD.R, man/nearPD.Rd (nearPD): new function built on Jens
22            Oehlschlaegel's ... result type still to be discussed!
23    
24    2007-08-10  Martin Maechler  <maechler@stat.math.ethz.ch>
25    
26            * man/image-methods.Rd: new, combining all image() methods
27    
28    2007-08-09  Martin Maechler  <maechler@stat.math.ethz.ch>
29    
30            * R/dgCMatrix.R: define qr() and lu() methods for "sparseMatrix"
31            to work via dgC...
32    
33            * R/Matrix.R (Matrix): special treatment for "table" (S3)
34    
35    2007-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
36    
37            * R/dgTMatrix.R (image): change defaults to
38                    aspect = "iso", colorkey = FALSE
39    
40    2007-08-06  Martin Maechler  <maechler@stat.math.ethz.ch>
41    
42            * src/dsyMatrix.c (dsyMatrix_matrix_mm): 'b' might be matrix;
43            must copy its *expanded* x slot before LAPACK call.
44    
45            * tests/matprod.R: test the last days' changes.
46    
47    2007-08-06 16:43  Douglas Bates <bates@stat.wisc.edu>
48    
49            * [r4712] inst/include/Matrix_stubs.c: Change R_cholmod_printf in stubs
50              as well as in sources
51            * [r4713] src/dsyMatrix.c: Duplicate the contents of the RHS before
52              Lapack call
53    
54    2007-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
55    
56            * R/Matrix.R (%*%, crossprod, tcrossprod): add method for
57                    ("Matrix", "matrix") which is needed in some cases.
58            Ditto for solve().
59    
60            * R/colSums.R (.as.dge.Fun): need ddenseMatrix methods to avoid
61            infinite recursion in dispatch for some cases.
62    
63    2007-08-02 08:48  Martin Maechler <maechler@stat.math.ethz.ch>
64    
65            * [r4693] src/chm_common.c: R_cholmod_printf() instead of Rprintf() just
66              so pointers match
67    
68    2007-08-02  Martin Maechler  <maechler@stat.math.ethz.ch>
69    
70            * DESCRIPTION (Date): set ready for release -- 0.999375-1
71    
72    2007-08-01 15:44  Douglas Bates <bates@stat.wisc.edu>
73    
74            * [r4686] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
75              src/chm_common.c, src/chm_common.h: Change API for
76              numeric_as_chm_dense and N_AS_CHM_DN
77    
78    2007-08-01  Martin Maechler  <maechler@stat.math.ethz.ch>
79    
80            * src/dtrMatrix.c (dtrMatrix_matrix_mm): fix dimensionality check (!)
81            * tests/matprod.R: regr.test for it
82    
83    2007-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
84    
85            * R/dMatrix.R: fix from Brian for   Math2(., digits = "missing")
86            * tests/group-methods.R: and regression-test it
87    
88    2007-07-19 19:45  Douglas Bates <bates@stat.wisc.edu>
89    
90            * [r4642] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
91              inst/include/cholmod.h, src/chm_common.c, src/init.c: Export
92              triplet_to_sparse, documentation, use typedefs
93    
94    2007-07-18  Martin Maechler  <maechler@stat.math.ethz.ch>
95    
96            * man/dpoMatrix-class.Rd: added 'corMatrix' example
97    
98            * src/dsyMatrix.[ch] (dsyMatrix_as_matrix): new 'keep_dimnames' arg
99            * src/dtrMatrix.[ch] (dtrMatrix_as_matrix): ditto
100            * src/init.c, R/dsyMatrix.R, R/dtrMatrix.R, R/lgTMatrix.R: ditto
101    
102            * R/lsparseMatrix.R: bug fix in "all" method
103            * R/Ops.R (.do.Logic.lsparse): "|" bug in borderline case
104    
105            * R/dsyMatrix.R (coerce->dsTMatrix): (i,j) slots should *not* have names
106            * R/ngTMatrix.R (coerce->ngTMatrix): ditto;
107                    + matrix |-> nMatrix coercion
108            * R/pMatrix.R: + setAs()  to dMatrix and from nMatrix
109            * man/pMatrix-class.Rd: ditto
110    
111            * R/Matrix.R (Summary): method for non-dMatrix
112    
113            * tests/Class+Meth.R (extraValid): new check about "dirty" slots
114            * tests/Class+Meth.R (tstMatrixClass): test norm(.);
115                    test all Summary methods.
116    
117    2007-07-16  Martin Maechler  <maechler@stat.math.ethz.ch>
118    
119            * R/dgeMatrix.R (norm, rcond): methods for 'matrix'
120    
121    2007-07-14  Martin Maechler  <maechler@stat.math.ethz.ch>
122    
123            * R/sparseMatrix.R (norm): simple methods for sparseMatrix
124    
125            * R/pMatrix.R (t?crossprod): methods for pMatrix
126    
127    2007-07-10  Douglas Bates  <bates@stat.wisc.edu>
128    
129            * src/dgeMatrix.c (dgeMatrix_colsums): Get the logic straight.
130    
131    2007-07-09 20:45  Douglas Bates <bates@stat.wisc.edu>
132    
133            * [r4579] src/dgeMatrix.c: Untangle horrible code in dgeMatrix_colsums
134              trying to fix a subtle bug - which has been somewhere else.
135    
136    2007-07-09 19:43  Martin Maechler <maechler@stat.math.ethz.ch>
137    
138            * [r4578] src/dgeMatrix.c: "cleaned" dgeMatrix_colsums() - but did not
139              solve the bug
140    
141    2007-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
142    
143            * src/dgCMatrix.c (compressed_to_TMatrix):
144    
145    2007-07-07  Martin Maechler  <maechler@stat.math.ethz.ch>
146    
147            * src/Csparse.c (Rsparse_validate): new, to have some validity
148            checking for RsparseMatrix
149            * src/dgCMatrix.c (xRMatrix_validate): ditto
150            * src/dtCMatrix.c (tRMatrix_validate): ditto
151    
152    2007-07-07  Douglas Bates <bates@stat.wisc.edu>
153    
154            * [r4567] R/AllClass.R: Slots already in RsparseMatrix were redefined in
155              lgRMatrix
156            * [r4568] DESCRIPTION: Prepare for bug-fix release
157            * [r4570] src/CHOLMOD/Check/cholmod_write.c: Include cholmod_matrixops.h
158              for declaration of cholmod_symmetry
159    
160    2007-07-06  Martin Maechler  <maechler@stat.math.ethz.ch>
161    
162            * DESCRIPTION (Version): 0.999375 merged into the trunk; ready for
163            release.
164    
165    2007-07-06 14:11  Douglas Bates <bates@stat.wisc.edu>
166    
167            * [r4559] src/iohb.c, src/iohb.h: Remove Harwell-Boeing input/output
168              functions - no longer used
169            * [r4560] src/HBMM.c, src/Mutils.c, src/dgTMatrix.c, src/dgeMatrix.c,
170              src/dspMatrix.c, src/dsyMatrix.c, src/dtCMatrix.c,
171              src/factorizations.c, src/sparseQR.c: Replace most calls to Calloc by
172              Alloca
173    
174    2007-07-06 13:14  Martin Maechler <maechler@stat.math.ethz.ch>
175    
176            * [r4558] inst/doc/Comparisons.Rnw, src/CHMfactor.c, src/Csparse.c,
177              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dense.c,
178              src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c, src/sparseQR.c,
179              src/t_gCMatrix_colSums.c: more R_CheckStack()s
180    
181    2007-07-05 18:12  Douglas Bates <bates@stat.wisc.edu>
182    
183            * [r4550] inst/include/Matrix.h: Add the macro N_AS_CHM_DN to "alloca"
184              the required amount of memory then call M_numeric_as_chm_dense.
185            * [r4556] src/Mutils.h, src/dgCMatrix.c: Define and use the Alloca macro
186              (like Calloc but calling alloca)
187    
188    2007-07-05  Martin Maechler  <maechler@stat.math.ethz.ch>
189    
190            * R/sparseMatrix.R (printSpMatrix): renamed from prSpMatrix()
191            and extended with more sophisticated 'col.names' option.
192            * NAMESPACE: export  printSparseMatrix()
193            * man/printSpMatrix.Rd: document, incl. examples
194    
195    2007-07-04 16:21  Douglas Bates <bates@stat.wisc.edu>
196    
197            * [r4543] src/cs_utils.c, src/cs_utils.h, src/dgCMatrix.c,
198              src/dtCMatrix.c, src/sparseQR.c: CSP typedef for *cs and macro
199              AS_CSP. API change - pass the empty structure to Matrix_as_cs.
200    
201    2007-07-04  Martin Maechler  <maechler@stat.math.ethz.ch>
202    
203            * DESCRIPTION (Version): 0.99875-4
204    
205            * tests/Class+Meth.R (tstMatrixClass): add dimnames, and hence test
206            some dimnames perservation.
207    
208            * R/dsTMatrix.R (t-method): keep dimnames
209            * R/dtTMatrix.R:  ditto
210    
211            * R/sparseMatrix.R (prSpMatrix): print colnames when non-trivial
212            and ncol(.) < 10
213    
214            * src/cs_utils.c: drop check_class() and use Matrix_check_class()
215            from Mutils.h
216    
217            * src/lgCMatrix.c ([ln]csc_to_matrix): no longer lose dimnames,
218            e.g. in as(<ngCMatrix>, "matrix")
219    
220    2007-07-01 13:27  Douglas Bates <bates@stat.wisc.edu>
221    
222            * [r4529] .: Create a branch for the API changes from the 0.99875
223              series to the 0.999375 series
224            * [r4530] DESCRIPTION, inst/include/Matrix.h,
225              inst/include/Matrix_stubs.c, src/CHMfactor.c, src/Csparse.c,
226              src/Mutils.h, src/Tsparse.c, src/chm_common.c, src/chm_common.h,
227              src/dense.c, src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c,
228              src/t_gCMatrix_colSums.c: API change - pass the empty structure to the
229              as_cholmod_x functions
230    
231    2007-06-30 09:05  Martin Maechler <maechler@stat.math.ethz.ch>
232    
233            * [r4527] trunk/Matrix/DESCRIPTION, trunk/Matrix/NAMESPACE,
234              trunk/Matrix/inst/doc/Comparisons.Rnw: add session- and hardware-info
235              to Comparisons
236    
237    >>>>>>> .merge-right.r4561
238    2007-06-29  Martin Maechler  <maechler@stat.math.ethz.ch>
239    
240            * DESCRIPTION (Version): 0.99875-3 ready to be released.
241    
242            * R/sparseMatrix.R (spMatrix): make spMatrix(3,4) working
243    
244            * R/AllGeneric.R: set "Math" (and "Math2") group generics in a way
245            that should also work in a future version of R.
246    
247    2007-06-21  Martin Maechler  <maechler@stat.math.ethz.ch>
248    
249            * NAMESPACE, R/AllClass.R: "xsparseVector" class union.
250    
251            * R/sparseVector.R: more *sparseVector coercions, notably for
252            non - double ones.
253    
254    2007-06-19  Martin Maechler  <maechler@stat.math.ethz.ch>
255    
256            * R/colSums.R: new file for all (col|row)(Sums|Means) methods,
257              notably the new ones building on the new .Call(.)s:
258    
259            * src/dgCMatrix.c (DEF_gCMatrix_COLSUMS): use to define
260            all 4 of [dlin]gCMatrix_colSums().
261    
262    2007-06-18 16:12  Douglas Bates <bates@stat.wisc.edu>
263    
264            * [r4472] src/Syms.h, src/init.c: Added Matrix_lengthSym
265            * [r4473] src/dgCMatrix.c: Modified dgCMatrix_colSums for sparseVector
266              result
267    
268    2007-06-16  Martin Maechler  <maechler@stat.math.ethz.ch>
269    
270            * R/kronecker.R: fix typo (could lead to inf.recursion)
271            * test/simple.R: testing that
272    
273            * R/sparseMatrix.R (prSpMatrix): change to be used as print()
274            method as well (which can have arguments, show() can't).
275    
276    2007-06-16 15:52  Douglas Bates <bates@stat.wisc.edu>
277    
278            * [r4466] R/dgCMatrix.R, src/dgCMatrix.c, src/dgCMatrix.h, src/init.c:
279              added dgCMatrix_colSums for [col,row][Sums,Means]
280    
281    2007-06-15 23:15  Douglas Bates <bates@stat.wisc.edu>
282    
283            * [r4460] R/sparseMatrix.R, man/dgCMatrix-class.Rd, src/dgCMatrix.c,
284              src/dgCMatrix.h, src/init.c: added lm.fit.sparse (unexported),
285              coercion of "factor" to "dgCMatrix" and dgCMatrix_cholsol
286            * [r4461] R/AllClass.R, man/sparseMatrix-class.Rd: draft "indicators"
287              class
288            * [r4463] R/sparseMatrix.R, man/dgCMatrix-class.Rd,
289              man/sparseMatrix-class.Rd: Don't need an "indicators" class - use the
290              row names to store the levels - duh!  Added an example.
291    
292    2007-06-14  Martin Maechler  <maechler@stat.math.ethz.ch>
293    
294            * src/Csparse.c (Csparse_validate): check for *repeated* entries
295            thanks to example from Christian Buchta; with a test here:
296            * tests/simple.R:
297    
298    2007-06-07  Martin Maechler  <maechler@stat.math.ethz.ch>
299    
300            * R/Auxiliaries.R (callGeneric): another fix, needed for some cases
301            of colSums(*, sparseResult = TRUE)
302    
303    2007-06-06  Martin Maechler  <maechler@stat.math.ethz.ch>
304    
305            * R/lsparseMatrix.R, R/ldenseMatrix.R (all, any): change default to
306            'na.rm = FALSE' as "everywhere" else in R.
307    
308  2007-06-05 Douglas Bates <bates@stat.wisc.edu>  2007-06-05 Douglas Bates <bates@stat.wisc.edu>
309    
310            * [r4421] src/CSparse_install.sh: Modify for new organization of
311              CSparse package
312          * [r4425] src/UFsparse_download.sh: Update to version 3.0.0 of          * [r4425] src/UFsparse_download.sh: Update to version 3.0.0 of
313            SuiteSparse            SuiteSparse
314          * [r4426] src/Makefile: add ./UFconfig to the include path for          * [r4426] src/Makefile: add ./UFconfig to the include path for
315            compilation            compilation
316          * [r4427] src/cs.c, src/cs.h: update to CSparse version 2.2.0          * [r4427] src/cs.[ch]: update to CSparse version 2.2.0
317          * [r4428] inst/doc/UFsparse/* src/AMD/* src/CHOLMOD/*          * [r4428] inst/doc/UFsparse/* src/{AMD,CHOLMOD,COLAMD}/*
318            src/COLAMD/* src/UFconfig/UFconfig.h: Update to version 3.0.0 of            src/UFconfig/UFconfig.h: Update to version 3.0.0 of SuiteSparse
           SuiteSparse  
319    
320  2007-06-05  Martin Maechler  <maechler@stat.math.ethz.ch>  2007-06-05  Martin Maechler  <maechler@stat.math.ethz.ch>
321    

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