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revision 1922, Sat Jun 23 18:08:48 2007 UTC revision 2073, Wed Sep 26 16:17:00 2007 UTC
# Line 1  Line 1 
1    2007-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * R/pMatrix.R (.m.mult.pMat): fix <matrix> %*% <pMatrix>,
4              thanks to Kasper Kristensen.
5            * tests/matprod.R: regression test for that.
6    
7    2007-09-23 17:32  Douglas Bates <bates@stat.wisc.edu>
8    
9            * [r4778] R/AllGeneric.R: Check R version before defining generics for
10              primitives
11    
12    2007-09-13  Martin Maechler  <maechler@stat.math.ethz.ch>
13    
14            * R/denseMatrix.R (rcond): method
15            * R/sparseQR.R (rcond): method, use x or t(x)
16    
17    2007-09-12  Martin Maechler  <maechler@stat.math.ethz.ch>
18    
19            * R/dgeMatrix.R (rcond): method: work via qr.R() for non-square
20            matrices.
21            * R/sparseMatrix.R: Ditto for all other rcond() method definitions.
22    
23            * man/rcond.Rd: mention the more general definition, and add
24            example for non-square matrices.
25    
26            * man/chol.Rd: new file, for the S4 chol() generic and all methods.
27    
28    2007-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
29    
30            * R/sparseQR.R: add qr.R() method [to be used for rcond()]
31    
32    2007-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
33    
34            * R/Matrix.R ([<-): add (Matrix,missing,ANY,Matrix) etc
35            * tests/indexing.R: add new regression for the above cases.
36    
37    2007-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
38    
39            * src/Mutils.h (__sun): clause for alloca.h on Solaris
40    
41    2007-08-16  Martin Maechler  <maechler@stat.math.ethz.ch>
42    
43            * DESCRIPTION (Date, Version): 0.999375-2
44    
45    2007-08-15  Martin Maechler  <maechler@stat.math.ethz.ch>
46    
47            * R/HBMM.R (readMM): make work for pattern matrices as well
48    
49    2007-08-14 13:07  Douglas Bates <bates@stat.wisc.edu>
50    
51            * [r4730] src/Mutils.h: declare alloca
52            * [r4734] NAMESPACE, R/AllGeneric.R, R/Csparse.R, R/HBMM.R, R/Tsparse.R,
53              R/dgCMatrix.R, R/dgTMatrix.R, R/dsCMatrix.R, R/dsTMatrix.R,
54              man/externalFormats.Rd, src/Csparse.c, src/Csparse.h, src/DEPS.mkf,
55              src/HBMM.c, src/HBMM.h, src/Mutils.h, src/SOURCES_C.mkf, src/init.c,
56              src/mmio.c, src/mmio.h: Remove deprecated function writeHB and its
57              methods; switch writeMM to use CHOLMOD code; repair readMM
58    
59    2007-08-14  Martin Maechler  <maechler@stat.math.ethz.ch>
60    
61            * R/nearPD.R, man/nearPD.Rd (nearPD): new function built on Jens
62            Oehlschlaegel's ... result type still to be discussed!
63    
64    2007-08-10  Martin Maechler  <maechler@stat.math.ethz.ch>
65    
66            * man/image-methods.Rd: new, combining all image() methods
67    
68    2007-08-09  Martin Maechler  <maechler@stat.math.ethz.ch>
69    
70            * R/dgCMatrix.R: define qr() and lu() methods for "sparseMatrix"
71            to work via dgC...
72    
73            * R/Matrix.R (Matrix): special treatment for "table" (S3)
74    
75    2007-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
76    
77            * R/dgTMatrix.R (image): change defaults to
78                    aspect = "iso", colorkey = FALSE
79    
80    2007-08-06  Martin Maechler  <maechler@stat.math.ethz.ch>
81    
82            * src/dsyMatrix.c (dsyMatrix_matrix_mm): 'b' might be matrix;
83            must copy its *expanded* x slot before LAPACK call.
84    
85            * tests/matprod.R: test the last days' changes.
86    
87    2007-08-06 16:43  Douglas Bates <bates@stat.wisc.edu>
88    
89            * [r4712] inst/include/Matrix_stubs.c: Change R_cholmod_printf in stubs
90              as well as in sources
91            * [r4713] src/dsyMatrix.c: Duplicate the contents of the RHS before
92              Lapack call
93    
94    2007-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
95    
96            * R/Matrix.R (%*%, crossprod, tcrossprod): add method for
97                    ("Matrix", "matrix") which is needed in some cases.
98            Ditto for solve().
99    
100            * R/colSums.R (.as.dge.Fun): need ddenseMatrix methods to avoid
101            infinite recursion in dispatch for some cases.
102    
103    2007-08-02 08:48  Martin Maechler <maechler@stat.math.ethz.ch>
104    
105            * [r4693] src/chm_common.c: R_cholmod_printf() instead of Rprintf() just
106              so pointers match
107    
108    2007-08-02  Martin Maechler  <maechler@stat.math.ethz.ch>
109    
110            * DESCRIPTION (Date): set ready for release -- 0.999375-1
111    
112    2007-08-01 15:44  Douglas Bates <bates@stat.wisc.edu>
113    
114            * [r4686] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
115              src/chm_common.c, src/chm_common.h: Change API for
116              numeric_as_chm_dense and N_AS_CHM_DN
117    
118    2007-08-01  Martin Maechler  <maechler@stat.math.ethz.ch>
119    
120            * src/dtrMatrix.c (dtrMatrix_matrix_mm): fix dimensionality check (!)
121            * tests/matprod.R: regr.test for it
122    
123    2007-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
124    
125            * R/dMatrix.R: fix from Brian for   Math2(., digits = "missing")
126            * tests/group-methods.R: and regression-test it
127    
128    2007-07-19 19:45  Douglas Bates <bates@stat.wisc.edu>
129    
130            * [r4642] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
131              inst/include/cholmod.h, src/chm_common.c, src/init.c: Export
132              triplet_to_sparse, documentation, use typedefs
133    
134    2007-07-18  Martin Maechler  <maechler@stat.math.ethz.ch>
135    
136            * man/dpoMatrix-class.Rd: added 'corMatrix' example
137    
138            * src/dsyMatrix.[ch] (dsyMatrix_as_matrix): new 'keep_dimnames' arg
139            * src/dtrMatrix.[ch] (dtrMatrix_as_matrix): ditto
140            * src/init.c, R/dsyMatrix.R, R/dtrMatrix.R, R/lgTMatrix.R: ditto
141    
142            * R/lsparseMatrix.R: bug fix in "all" method
143            * R/Ops.R (.do.Logic.lsparse): "|" bug in borderline case
144    
145            * R/dsyMatrix.R (coerce->dsTMatrix): (i,j) slots should *not* have names
146            * R/ngTMatrix.R (coerce->ngTMatrix): ditto;
147                    + matrix |-> nMatrix coercion
148            * R/pMatrix.R: + setAs()  to dMatrix and from nMatrix
149            * man/pMatrix-class.Rd: ditto
150    
151            * R/Matrix.R (Summary): method for non-dMatrix
152    
153            * tests/Class+Meth.R (extraValid): new check about "dirty" slots
154            * tests/Class+Meth.R (tstMatrixClass): test norm(.);
155                    test all Summary methods.
156    
157    2007-07-16  Martin Maechler  <maechler@stat.math.ethz.ch>
158    
159            * R/dgeMatrix.R (norm, rcond): methods for 'matrix'
160    
161    2007-07-14  Martin Maechler  <maechler@stat.math.ethz.ch>
162    
163            * R/sparseMatrix.R (norm): simple methods for sparseMatrix
164    
165            * R/pMatrix.R (t?crossprod): methods for pMatrix
166    
167    2007-07-10  Douglas Bates  <bates@stat.wisc.edu>
168    
169            * src/dgeMatrix.c (dgeMatrix_colsums): Get the logic straight.
170    
171    2007-07-09 20:45  Douglas Bates <bates@stat.wisc.edu>
172    
173            * [r4579] src/dgeMatrix.c: Untangle horrible code in dgeMatrix_colsums
174              trying to fix a subtle bug - which has been somewhere else.
175    
176    2007-07-09 19:43  Martin Maechler <maechler@stat.math.ethz.ch>
177    
178            * [r4578] src/dgeMatrix.c: "cleaned" dgeMatrix_colsums() - but did not
179              solve the bug
180    
181    2007-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
182    
183            * src/dgCMatrix.c (compressed_to_TMatrix):
184    
185    2007-07-07  Martin Maechler  <maechler@stat.math.ethz.ch>
186    
187            * src/Csparse.c (Rsparse_validate): new, to have some validity
188            checking for RsparseMatrix
189            * src/dgCMatrix.c (xRMatrix_validate): ditto
190            * src/dtCMatrix.c (tRMatrix_validate): ditto
191    
192    2007-07-07  Douglas Bates <bates@stat.wisc.edu>
193    
194            * [r4567] R/AllClass.R: Slots already in RsparseMatrix were redefined in
195              lgRMatrix
196            * [r4568] DESCRIPTION: Prepare for bug-fix release
197            * [r4570] src/CHOLMOD/Check/cholmod_write.c: Include cholmod_matrixops.h
198              for declaration of cholmod_symmetry
199    
200    2007-07-06  Martin Maechler  <maechler@stat.math.ethz.ch>
201    
202            * DESCRIPTION (Version): 0.999375 merged into the trunk; ready for
203            release.
204    
205    2007-07-06 14:11  Douglas Bates <bates@stat.wisc.edu>
206    
207            * [r4559] src/iohb.c, src/iohb.h: Remove Harwell-Boeing input/output
208              functions - no longer used
209            * [r4560] src/HBMM.c, src/Mutils.c, src/dgTMatrix.c, src/dgeMatrix.c,
210              src/dspMatrix.c, src/dsyMatrix.c, src/dtCMatrix.c,
211              src/factorizations.c, src/sparseQR.c: Replace most calls to Calloc by
212              Alloca
213    
214    2007-07-06 13:14  Martin Maechler <maechler@stat.math.ethz.ch>
215    
216            * [r4558] inst/doc/Comparisons.Rnw, src/CHMfactor.c, src/Csparse.c,
217              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dense.c,
218              src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c, src/sparseQR.c,
219              src/t_gCMatrix_colSums.c: more R_CheckStack()s
220    
221    2007-07-05 18:12  Douglas Bates <bates@stat.wisc.edu>
222    
223            * [r4550] inst/include/Matrix.h: Add the macro N_AS_CHM_DN to "alloca"
224              the required amount of memory then call M_numeric_as_chm_dense.
225            * [r4556] src/Mutils.h, src/dgCMatrix.c: Define and use the Alloca macro
226              (like Calloc but calling alloca)
227    
228    2007-07-05  Martin Maechler  <maechler@stat.math.ethz.ch>
229    
230            * R/sparseMatrix.R (printSpMatrix): renamed from prSpMatrix()
231            and extended with more sophisticated 'col.names' option.
232            * NAMESPACE: export  printSparseMatrix()
233            * man/printSpMatrix.Rd: document, incl. examples
234    
235    2007-07-04 16:21  Douglas Bates <bates@stat.wisc.edu>
236    
237            * [r4543] src/cs_utils.c, src/cs_utils.h, src/dgCMatrix.c,
238              src/dtCMatrix.c, src/sparseQR.c: CSP typedef for *cs and macro
239              AS_CSP. API change - pass the empty structure to Matrix_as_cs.
240    
241    2007-07-04  Martin Maechler  <maechler@stat.math.ethz.ch>
242    
243            * DESCRIPTION (Version): 0.99875-4
244    
245            * tests/Class+Meth.R (tstMatrixClass): add dimnames, and hence test
246            some dimnames perservation.
247    
248            * R/dsTMatrix.R (t-method): keep dimnames
249            * R/dtTMatrix.R:  ditto
250    
251            * R/sparseMatrix.R (prSpMatrix): print colnames when non-trivial
252            and ncol(.) < 10
253    
254            * src/cs_utils.c: drop check_class() and use Matrix_check_class()
255            from Mutils.h
256    
257            * src/lgCMatrix.c ([ln]csc_to_matrix): no longer lose dimnames,
258            e.g. in as(<ngCMatrix>, "matrix")
259    
260    2007-07-01 13:27  Douglas Bates <bates@stat.wisc.edu>
261    
262            * [r4529] .: Create a branch for the API changes from the 0.99875
263              series to the 0.999375 series
264            * [r4530] DESCRIPTION, inst/include/Matrix.h,
265              inst/include/Matrix_stubs.c, src/CHMfactor.c, src/Csparse.c,
266              src/Mutils.h, src/Tsparse.c, src/chm_common.c, src/chm_common.h,
267              src/dense.c, src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c,
268              src/t_gCMatrix_colSums.c: API change - pass the empty structure to the
269              as_cholmod_x functions
270    
271    2007-06-30 09:05  Martin Maechler <maechler@stat.math.ethz.ch>
272    
273            * [r4527] trunk/Matrix/DESCRIPTION, trunk/Matrix/NAMESPACE,
274              trunk/Matrix/inst/doc/Comparisons.Rnw: add session- and hardware-info
275              to Comparisons
276    
277    >>>>>>> .merge-right.r4561
278    2007-06-29  Martin Maechler  <maechler@stat.math.ethz.ch>
279    
280            * DESCRIPTION (Version): 0.99875-3 ready to be released.
281    
282            * R/sparseMatrix.R (spMatrix): make spMatrix(3,4) working
283    
284            * R/AllGeneric.R: set "Math" (and "Math2") group generics in a way
285            that should also work in a future version of R.
286    
287  2007-06-21  Martin Maechler  <maechler@stat.math.ethz.ch>  2007-06-21  Martin Maechler  <maechler@stat.math.ethz.ch>
288    
289          * NAMESPACE, R/AllClass.R: "xsparseVector" class union.          * NAMESPACE, R/AllClass.R: "xsparseVector" class union.
# Line 5  Line 291 
291          * R/sparseVector.R: more *sparseVector coercions, notably for          * R/sparseVector.R: more *sparseVector coercions, notably for
292          non - double ones.          non - double ones.
293    
   
294  2007-06-19  Martin Maechler  <maechler@stat.math.ethz.ch>  2007-06-19  Martin Maechler  <maechler@stat.math.ethz.ch>
295    
296          * R/colSums.R: new file for all (col|row)(Sums|Means) methods,          * R/colSums.R: new file for all (col|row)(Sums|Means) methods,

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