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revision 1548, Mon Sep 11 22:13:07 2006 UTC revision 1665, Fri Nov 3 23:18:07 2006 UTC
# Line 1  Line 1 
1    2006-11-03  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * src/dsCMatrix.c (dsCMatrix_Csparse_solve): new
4            * R/dsCMatrix.R (solve): "fully-sparse" using the above.
5    
6            * R/AllClass.R: "pMatrix" now also inherits from "generalMatrix"
7    
8            * tests/Class+Meth.R (tstMatrixClass): now assure
9            the (important in method programming) property :
10    
11                    ###>>  Every "Matrix" is either
12                    ###>>  "general*", "symmetric*", "triangular*" or "diagonal*"
13    
14                    (where "*" stands for "Matrix")
15    
16            * R/Auxiliaries.R (diagU2N): now .Call()s Csparse_diagU2N for <Csparse>
17    
18            * R/dMatrix.R (Compare(<dMatrix>,<dMatrix>): update and
19            * tests/validObj.R: checks for "comparison"
20    
21            * R/sparseMatrix.R ([): improved indexing for sparse;
22                    trying to keep <symmetric>[ n, n] symmmetric
23    
24            * tests/indexing.R: indexing for logical sparse now ok
25    
26    
27    
28    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
29    
30            * src/Tsparse.c: use xTsparse_validate() , and hence remove
31    
32            * src/{ltC,lsC,lgT}Matrix.[ch]: removed
33    
34    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
35    
36            * R/AllClass.R (Matrix-class): check length of dimnames in validity.
37    
38            * tests/simple.R: validObject() checking the above.
39    
40            * src/dgCMatrix.c (xCMatrix_validate): new, small and simple,
41            replacing both dgCMatrix_validate and lgCM*.
42    
43            * src/Csparse.c (Csparse_dense_prod, etc): do not lose dimnames;
44            fix dimnames setting in other places.
45            * src/chm_common.c (chm_dense_to_SEXP): now can pass dimnames
46    
47    2006-11-01  Martin Maechler  <maechler@stat.math.ethz.ch>
48    
49            * R/Csparse.R,src/Csparse.c, etc: tcrossprod(<CsparseM>,<CsparseM>)
50    
51            * R/sparseMatrix.R (isSymmetric): drop 'factors' slot for
52            symmetry test, via
53            * R/Auxiliaries.R (.as.dgC.0.factors):
54    
55    2006-11-01  Douglas Bates  <bates@r-project.org>
56    
57            * R/Csparse.R,src/Csparse.c,tests/matprod.R,
58            man/CsparseMatrix-class.Rd: crossprod(<CsparseMatrix>,
59            <CsparseMatrix>) added
60    
61    2006-10-30  Martin Maechler  <maechler@stat.math.ethz.ch>
62    
63            * tests/matprod.R: add a variation of Harri's example
64    
65            * R/dsparseMatrix.R: fix crossprod(<dsparse>, <dge>) to *not*
66            recursive infinitely.
67    
68            * R/dgCMatrix.R: + solve(<sparse>, <sparse>)
69    
70            * tests/indexing.R: add test for the "<" bug fixed 10-27 in R/dMatrix.R
71    
72    2006-10-28  Martin Maechler  <maechler@stat.math.ethz.ch>
73    
74            * tests/Class+Meth.R (tstMatrixClass): more: use non-trivial
75            matrix if possible; test m+m == 2*m; now test dgRMatrix.
76            * R/dgRMatrix.R (.to.dgR): a few more coercions, in order to
77            satisfy the above test.
78    
79    2006-10-27  Martin Maechler  <maechler@stat.math.ethz.ch>
80    
81            * R/Matrix.R (Ops):  <Matrix> o <matrix>  method added
82    
83            * R/dgCMatrix.R: solve(a, b="missing") based on
84            * src/dgCMatrix.c (dgCMatrix_matrix_solve): extend to work with
85            RHS = NULL.
86    
87            * R/diagMatrix.R (diagdiagprod): extend %*% etc to ldiMatrix;
88            add more (needed) [t]crossprod() methods.
89    
90            * man/ddiMatrix-class.Rd: more info, notably on 'diag'
91    
92            * R/Auxiliaries.R (as_CspClass): cleanup
93            (drop0): internal utility for "Csparse_drop(*, 0)"
94            (.bail.out.2): encourage active feedback
95    
96    2006-10-26  Martin Maechler  <maechler@stat.math.ethz.ch>
97    
98            * R/dMatrix.R(Compare): new(), then slots [no validity check]
99    
100            * src/Csparse.c (Csparse_validate): fixed (and more efficient in
101            non-valid or 'sorted' case).
102    
103            * R/dsparseMatrix.R: add "chol" method.
104            * R/ddenseMatrix.R: ditto
105    
106            * R/diagMatrix.R (Ops): group methods for  <diagonal> o <sparse>
107            * NAMESPACE (Ops)
108            * R/diagMatrix.R (diag2T): simple utility used "higher level"
109            coercion; deprecating direct lower level coercions.
110    
111            * R/*.R (seq): use seq_len() and seq_along() where possible.
112    
113    
114    2006-10-23  Martin Maechler  <maechler@stat.math.ethz.ch>
115    
116            * DESCRIPTION (Version): 0.9975-5 ready for release
117    
118    2006-10-20  Douglas Bates  <bates@stat.wisc.edu>
119    
120            * src/init.c (R_init_Matrix): export more cholmod CCallable functions.
121    
122    2006-10-20  Martin Maechler  <maechler@stat.math.ethz.ch>
123    
124            * R/AllClass.R (corMatrix): add 'validity' check;
125                    comment out unused "LDL" class definition
126            * NAMESPACE: mention, but do not export "LDL" class
127            * R/corMatrix.R: new (simple), needed for R-devel with
128            * tests/Class+Meth.R (tstMatrixClass): 1 exception for corMatrix
129              coerce and t() exceptions for all 5 'Mat.MatFact' classes.
130    
131    2006-10-19  Douglas Bates  <bates@stat.wisc.edu>
132    
133            * src/chm_common.h: Add R_cholmod_start to initialize cholmod to
134            use Rprintf and R's error handling.
135    
136    2006-10-17  Martin Maechler  <maechler@stat.math.ethz.ch>
137    
138            * R/diagMatrix.R (%*%): rep(*, each = .) in Matrix %*% diagonal.
139            * tests/matprod.R: add tests for the bug fixed.
140    
141    2006-10-11  Douglas Bates  <bates@stat.wisc.edu>
142    
143            * src/HBMM.[ch]: remove HarwellBoeing format for writing.
144            * src/SOURCES_C.mkf (SOURCES_C): no longer compile iohb.c
145    
146    2006-10-06  Douglas Bates  <bates@stat.wisc.edu>
147    
148            * R/d[gs]CMatrix.R: deprecate the writeHB function.  Use writeMM instead.
149    
150    2006-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
151    
152            * DESCRIPTION (Version): 0.9975-3
153    
154            * R/diagMatrix.R (bdiag): new function constructing block diagonal
155            (sparse) matrices.
156            * man/bdiag.Rd: docu + examples
157    
158            * R/Csparse.R (replCmat): calling new Csparse_drop() now.
159    
160            * src/Csparse.c (Csparse_general_to_symmetric, Csparse_drop): new functions
161            * R/lsCMatrix.R: three more coercions to lsC (thanks to the above)
162    
163            * R/diagMatrix.R (Diagonal): '[<-' method for diag.matrices such
164            that result is sparse or diagonal (and not dense).
165    
166            * man/Subassign-methods.Rd: fix examples
167    
168            * R/Matrix.R (Matrix):  Matrix(0, *) or Matrix(*, sparse=TRUE)
169            should always return a sparse (and not sometimes a diagonal) matrix.
170    
171    2006-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
172    
173            * R/Matrix.R ([<-): also for value "Matrix" or "matrix"
174    
175    2006-10-04  Douglas Bates  <bates@stat.wisc.edu>
176    
177            * DESCRIPTION (Version): 0.9975-2
178    
179            * inst/include/Matrix_stubs.c (M_cholmod_sparse_to_triplet): export more symbols
180    
181    2006-10-02  Douglas Bates  <bates@R-project.org>
182    
183            * tests/dg_Matrix.R: Simplify test taking into account new code.
184    
185    2006-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
186    
187            * R/Csparse.R (replCmat): improve for missing i / j in non-simple cases
188    
189            * R/lsTMatrix.R: new files w/ missing methods
190            * R/nsTMatrix.R:  "  'for completeness'
191    
192            * tests/Class+Meth.R: a bit less 'not.ok.classes'
193    
194            * R/Tsparse.R (t): generalized "t" method from "dgT*" to "Tsparse*"
195    
196    
197    2006-09-28  Douglas Bates  <bates@R-project.org>
198    
199            * src/dppMatrix.h: Ensure definition of dspMatrix_validate is
200            included.
201    
202            * src/init.c, inst/include/{Matrix.h,Matrix_stubs.h,cholmod.h}:
203            Export C-callable functions used in Zt_create in lme4.
204    
205    2006-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
206    
207            * DESCRIPTION (Version): 0.9975-1
208    
209            * tests/simple.R: less checks fail; using NA, found that our
210                    kronecker() is not base-compatible with NA's.
211    
212            * R/dMatrix.R: "Compare" method now implemented for all cases
213    
214            * R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility
215    
216            * man/dtpMatrix-class.Rd: mention length of 'x' slot
217    
218            * src/dtpMatrix.c (dtpMatrix_validate): fix check
219            * src/dspMatrix.c (dspMatrix_validate): ditto
220    
221            * R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
222              including coercion to [nl]tTMatrix.
223    
224            * R/diagMatrix.R (show): print a header line as for other classes.
225    
226    2006-09-27  Martin Maechler  <maechler@stat.math.ethz.ch>
227    
228            * src/Makefile.win (SUBDIRS): fix typo
229    
230    2006-09-19  Martin Maechler  <maechler@stat.math.ethz.ch>
231    
232            * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
233    
234    2006-09-18  Douglas Bates  <bates@stat.wisc.edu>
235    
236            * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
237            symmetric and y missing in R code using %*% (cholmod_aat doesn't
238            accept a symmetric matrix).
239            * tests/group-methods.R: Uncomment test of crossprod applied to
240            lsCMatrix objects.
241    
242    2006-09-18  Martin Maechler  <maechler@stat.math.ethz.ch>
243    
244            * R/AllClass.R (symmetricMatrix): add validity method (available
245            in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
246    
247            * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
248    
249            * tests/indexing.Rout.save:
250            * tests/indexing.R: additions, mainly for 'lsparse'
251    
252            * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
253            case.
254    
255            * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
256    
257    2006-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
258    
259            * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
260                    as 'N' (1-letter - Ok?)
261    
262            * tests/group-methods.R: add test for logical + NAs
263    
264            * R/dMatrix.R ("Compare"): fix to work with NA's
265    
266            * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
267    
268            * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
269                    which is implemented.
270    
271    2006-09-15  Martin Maechler  <maechler@stat.math.ethz.ch>
272    
273            * src/chm_common.c: coerce logical <-> double instead of
274            typecasting;  needed for "l" matrix handling in cholmod.
275    
276            * tests/other-pkgs.R (graph): small extension in "graph" checks.
277    
278            * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
279            (Tsp2grNEL): other fixes needed
280    
281  2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
282    
283          * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"          * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
# Line 7  Line 287 
287          * tests/: adaptions          * tests/: adaptions
288          * src/chm_common.c (chm_dense_to_SEXP): and others:          * src/chm_common.c (chm_dense_to_SEXP): and others:
289                  new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL                  new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
290          * src/Csparse.c, etc: dito          * src/Csparse.c, etc: ditto
291    
292  2006-09-11  Douglas Bates  <bates@R-project.org>  2006-09-11  Douglas Bates  <bates@R-project.org>
293    
# Line 26  Line 306 
306          * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()          * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
307    
308          * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"          * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
309          * man/tcrossprod.Rd: dito          * man/tcrossprod.Rd: ditto
310    
311  2006-09-08  Douglas Bates  <bates@stat.wisc.edu>  2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
312    
# Line 69  Line 349 
349    
350          * R/sparseMatrix.R (Arith): moved Arith group method one-level up          * R/sparseMatrix.R (Arith): moved Arith group method one-level up
351          from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"          from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
352          * R/dsparseMatrix.R: dito          * R/dsparseMatrix.R: ditto
353          * R/Csparse.R: dito          * R/Csparse.R: ditto
354    
355  2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
356    
# Line 86  Line 366 
366    
367          * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's          * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
368          * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.          * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
369          (.is.diagonal): dito          (.is.diagonal): ditto
370    
371          * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's          * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
372    

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