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revision 1548, Mon Sep 11 22:13:07 2006 UTC revision 1681, Wed Nov 29 15:55:03 2006 UTC
# Line 1  Line 1 
1    2006-11-29  Douglas Bates  <bates@stat.wisc.edu>
2    
3            * src/dgeMatrix.c (dgeMatrix_solve): Check error code from dgetri.
4            * tests/dg_Matrix.R: Add Barry Rowlingson's test of a matrix that
5            is exactly singular.
6    
7    2006-11-07  Martin Maechler  <maechler@stat.math.ethz.ch>
8    
9            * DESCRIPTION (Date): updated -> release 0.9975-6
10    
11    2006-11-06  Martin Maechler  <maechler@stat.math.ethz.ch>
12    
13            * R/Csparse.R (replCmat): symmetric indexing of symmetric matrix
14            now returns symmetric.
15    
16            * R/zzz.R ("diag<-"): replace "diag<-" in base for R <= 2.4.x
17    
18            * R/Matrix.R (.M.sub.i.2col):  new, for  M[ cbind(i,j) ] indexing.
19            * R/Matrix.R (.M.repl.i.2col): new, for  M[ cbind(i,j) ] <- value
20    
21            * R/Auxiliaries.R (.type.kind): added
22    
23    2006-11-04  Martin Maechler  <maechler@stat.math.ethz.ch>
24    
25            * src/cs.[ch]: updated to CSparse Version 2.0.3 by simply
26            running src/CSparse_install.sh
27    
28            * R/denseMatrix.R: "[": keep symmetric on symmetric indexing.
29    
30    2006-11-03  Martin Maechler  <maechler@stat.math.ethz.ch>
31    
32            * src/dsCMatrix.c (dsCMatrix_Csparse_solve): new
33            * R/dsCMatrix.R (solve): "fully-sparse" using the above.
34    
35            * R/AllClass.R: "pMatrix" now also inherits from "generalMatrix"
36    
37            * tests/Class+Meth.R (tstMatrixClass): now assure
38            the (important in method programming) property :
39    
40                    ###>>  Every "Matrix" is either
41                    ###>>  "general*", "symmetric*", "triangular*" or "diagonal*"
42    
43                    (where "*" stands for "Matrix")
44    
45            * R/Auxiliaries.R (diagU2N): now .Call()s Csparse_diagU2N for <Csparse>
46    
47            * R/dMatrix.R (Compare(<dMatrix>,<dMatrix>): update and
48            * tests/validObj.R: checks for "comparison"
49    
50            * R/sparseMatrix.R ([): improved indexing for sparse;
51                    trying to keep <symmetric>[ n, n] symmmetric
52    
53            * tests/indexing.R: indexing for logical sparse now ok
54    
55    
56    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
57    
58            * src/Tsparse.c: use xTsparse_validate() , and hence remove
59    
60            * src/{ltC,lsC,lgT}Matrix.[ch]: removed
61    
62    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
63    
64            * R/AllClass.R (Matrix-class): check length of dimnames in validity.
65    
66            * tests/simple.R: validObject() checking the above.
67    
68            * src/dgCMatrix.c (xCMatrix_validate): new, small and simple,
69            replacing both dgCMatrix_validate and lgCM*.
70    
71            * src/Csparse.c (Csparse_dense_prod, etc): do not lose dimnames;
72            fix dimnames setting in other places.
73            * src/chm_common.c (chm_dense_to_SEXP): now can pass dimnames
74    
75    2006-11-01  Martin Maechler  <maechler@stat.math.ethz.ch>
76    
77            * R/Csparse.R,src/Csparse.c, etc: tcrossprod(<CsparseM>,<CsparseM>)
78    
79            * R/sparseMatrix.R (isSymmetric): drop 'factors' slot for
80            symmetry test, via
81            * R/Auxiliaries.R (.as.dgC.0.factors):
82    
83    2006-11-01  Douglas Bates  <bates@r-project.org>
84    
85            * R/Csparse.R,src/Csparse.c,tests/matprod.R,
86            man/CsparseMatrix-class.Rd: crossprod(<CsparseMatrix>,
87            <CsparseMatrix>) added
88    
89    2006-10-30  Martin Maechler  <maechler@stat.math.ethz.ch>
90    
91            * tests/matprod.R: add a variation of Harri's example
92    
93            * R/dsparseMatrix.R: fix crossprod(<dsparse>, <dge>) to *not*
94            recursive infinitely.
95    
96            * R/dgCMatrix.R: + solve(<sparse>, <sparse>)
97    
98            * tests/indexing.R: add test for the "<" bug fixed 10-27 in R/dMatrix.R
99    
100    2006-10-28  Martin Maechler  <maechler@stat.math.ethz.ch>
101    
102            * tests/Class+Meth.R (tstMatrixClass): more: use non-trivial
103            matrix if possible; test m+m == 2*m; now test dgRMatrix.
104            * R/dgRMatrix.R (.to.dgR): a few more coercions, in order to
105            satisfy the above test.
106    
107    2006-10-27  Martin Maechler  <maechler@stat.math.ethz.ch>
108    
109            * R/Matrix.R (Ops):  <Matrix> o <matrix>  method added
110    
111            * R/dgCMatrix.R: solve(a, b="missing") based on
112            * src/dgCMatrix.c (dgCMatrix_matrix_solve): extend to work with
113            RHS = NULL.
114    
115            * R/diagMatrix.R (diagdiagprod): extend %*% etc to ldiMatrix;
116            add more (needed) [t]crossprod() methods.
117    
118            * man/ddiMatrix-class.Rd: more info, notably on 'diag'
119    
120            * R/Auxiliaries.R (as_CspClass): cleanup
121            (drop0): internal utility for "Csparse_drop(*, 0)"
122            (.bail.out.2): encourage active feedback
123    
124    2006-10-26  Martin Maechler  <maechler@stat.math.ethz.ch>
125    
126            * R/dMatrix.R(Compare): new(), then slots [no validity check]
127    
128            * src/Csparse.c (Csparse_validate): fixed (and more efficient in
129            non-valid or 'sorted' case).
130    
131            * R/dsparseMatrix.R: add "chol" method.
132            * R/ddenseMatrix.R: ditto
133    
134            * R/diagMatrix.R (Ops): group methods for  <diagonal> o <sparse>
135            * NAMESPACE (Ops)
136            * R/diagMatrix.R (diag2T): simple utility used "higher level"
137            coercion; deprecating direct lower level coercions.
138    
139            * R/*.R (seq): use seq_len() and seq_along() where possible.
140    
141    
142    2006-10-23  Martin Maechler  <maechler@stat.math.ethz.ch>
143    
144            * DESCRIPTION (Version): 0.9975-5 ready for release
145    
146    2006-10-20  Douglas Bates  <bates@stat.wisc.edu>
147    
148            * src/init.c (R_init_Matrix): export more cholmod CCallable functions.
149    
150    2006-10-20  Martin Maechler  <maechler@stat.math.ethz.ch>
151    
152            * R/AllClass.R (corMatrix): add 'validity' check;
153                    comment out unused "LDL" class definition
154            * NAMESPACE: mention, but do not export "LDL" class
155            * R/corMatrix.R: new (simple), needed for R-devel with
156            * tests/Class+Meth.R (tstMatrixClass): 1 exception for corMatrix
157              coerce and t() exceptions for all 5 'Mat.MatFact' classes.
158    
159    2006-10-19  Douglas Bates  <bates@stat.wisc.edu>
160    
161            * src/chm_common.h: Add R_cholmod_start to initialize cholmod to
162            use Rprintf and R's error handling.
163    
164    2006-10-17  Martin Maechler  <maechler@stat.math.ethz.ch>
165    
166            * R/diagMatrix.R (%*%): rep(*, each = .) in Matrix %*% diagonal.
167            * tests/matprod.R: add tests for the bug fixed.
168    
169    2006-10-11  Douglas Bates  <bates@stat.wisc.edu>
170    
171            * src/HBMM.[ch]: remove HarwellBoeing format for writing.
172            * src/SOURCES_C.mkf (SOURCES_C): no longer compile iohb.c
173    
174    2006-10-06  Douglas Bates  <bates@stat.wisc.edu>
175    
176            * R/d[gs]CMatrix.R: deprecate the writeHB function.  Use writeMM instead.
177    
178    2006-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
179    
180            * DESCRIPTION (Version): 0.9975-3
181    
182            * R/diagMatrix.R (bdiag): new function constructing block diagonal
183            (sparse) matrices.
184            * man/bdiag.Rd: docu + examples
185    
186            * R/Csparse.R (replCmat): calling new Csparse_drop() now.
187    
188            * src/Csparse.c (Csparse_general_to_symmetric, Csparse_drop): new functions
189            * R/lsCMatrix.R: three more coercions to lsC (thanks to the above)
190    
191            * R/diagMatrix.R (Diagonal): '[<-' method for diag.matrices such
192            that result is sparse or diagonal (and not dense).
193    
194            * man/Subassign-methods.Rd: fix examples
195    
196            * R/Matrix.R (Matrix):  Matrix(0, *) or Matrix(*, sparse=TRUE)
197            should always return a sparse (and not sometimes a diagonal) matrix.
198    
199    2006-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
200    
201            * R/Matrix.R ([<-): also for value "Matrix" or "matrix"
202    
203    2006-10-04  Douglas Bates  <bates@stat.wisc.edu>
204    
205            * DESCRIPTION (Version): 0.9975-2
206    
207            * inst/include/Matrix_stubs.c (M_cholmod_sparse_to_triplet): export more symbols
208    
209    2006-10-02  Douglas Bates  <bates@R-project.org>
210    
211            * tests/dg_Matrix.R: Simplify test taking into account new code.
212    
213    2006-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
214    
215            * R/Csparse.R (replCmat): improve for missing i / j in non-simple cases
216    
217            * R/lsTMatrix.R: new files w/ missing methods
218            * R/nsTMatrix.R:  "  'for completeness'
219    
220            * tests/Class+Meth.R: a bit less 'not.ok.classes'
221    
222            * R/Tsparse.R (t): generalized "t" method from "dgT*" to "Tsparse*"
223    
224    
225    2006-09-28  Douglas Bates  <bates@R-project.org>
226    
227            * src/dppMatrix.h: Ensure definition of dspMatrix_validate is
228            included.
229    
230            * src/init.c, inst/include/{Matrix.h,Matrix_stubs.h,cholmod.h}:
231            Export C-callable functions used in Zt_create in lme4.
232    
233    2006-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
234    
235            * DESCRIPTION (Version): 0.9975-1
236    
237            * tests/simple.R: less checks fail; using NA, found that our
238                    kronecker() is not base-compatible with NA's.
239    
240            * R/dMatrix.R: "Compare" method now implemented for all cases
241    
242            * R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility
243    
244            * man/dtpMatrix-class.Rd: mention length of 'x' slot
245    
246            * src/dtpMatrix.c (dtpMatrix_validate): fix check
247            * src/dspMatrix.c (dspMatrix_validate): ditto
248    
249            * R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
250              including coercion to [nl]tTMatrix.
251    
252            * R/diagMatrix.R (show): print a header line as for other classes.
253    
254    2006-09-27  Martin Maechler  <maechler@stat.math.ethz.ch>
255    
256            * src/Makefile.win (SUBDIRS): fix typo
257    
258    2006-09-19  Martin Maechler  <maechler@stat.math.ethz.ch>
259    
260            * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
261    
262    2006-09-18  Douglas Bates  <bates@stat.wisc.edu>
263    
264            * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
265            symmetric and y missing in R code using %*% (cholmod_aat doesn't
266            accept a symmetric matrix).
267            * tests/group-methods.R: Uncomment test of crossprod applied to
268            lsCMatrix objects.
269    
270    2006-09-18  Martin Maechler  <maechler@stat.math.ethz.ch>
271    
272            * R/AllClass.R (symmetricMatrix): add validity method (available
273            in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
274    
275            * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
276    
277            * tests/indexing.Rout.save:
278            * tests/indexing.R: additions, mainly for 'lsparse'
279    
280            * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
281            case.
282    
283            * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
284    
285    2006-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
286    
287            * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
288                    as 'N' (1-letter - Ok?)
289    
290            * tests/group-methods.R: add test for logical + NAs
291    
292            * R/dMatrix.R ("Compare"): fix to work with NA's
293    
294            * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
295    
296            * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
297                    which is implemented.
298    
299    2006-09-15  Martin Maechler  <maechler@stat.math.ethz.ch>
300    
301            * src/chm_common.c: coerce logical <-> double instead of
302            typecasting;  needed for "l" matrix handling in cholmod.
303    
304            * tests/other-pkgs.R (graph): small extension in "graph" checks.
305    
306            * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
307            (Tsp2grNEL): other fixes needed
308    
309  2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
310    
311          * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"          * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
# Line 7  Line 315 
315          * tests/: adaptions          * tests/: adaptions
316          * src/chm_common.c (chm_dense_to_SEXP): and others:          * src/chm_common.c (chm_dense_to_SEXP): and others:
317                  new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL                  new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
318          * src/Csparse.c, etc: dito          * src/Csparse.c, etc: ditto
319    
320  2006-09-11  Douglas Bates  <bates@R-project.org>  2006-09-11  Douglas Bates  <bates@R-project.org>
321    
# Line 26  Line 334 
334          * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()          * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
335    
336          * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"          * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
337          * man/tcrossprod.Rd: dito          * man/tcrossprod.Rd: ditto
338    
339  2006-09-08  Douglas Bates  <bates@stat.wisc.edu>  2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
340    
# Line 69  Line 377 
377    
378          * R/sparseMatrix.R (Arith): moved Arith group method one-level up          * R/sparseMatrix.R (Arith): moved Arith group method one-level up
379          from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"          from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
380          * R/dsparseMatrix.R: dito          * R/dsparseMatrix.R: ditto
381          * R/Csparse.R: dito          * R/Csparse.R: ditto
382    
383  2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
384    
# Line 86  Line 394 
394    
395          * 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
396          * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.          * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
397          (.is.diagonal): dito          (.is.diagonal): ditto
398    
399          * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's          * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
400    

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