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revision 1577, Mon Sep 18 21:01:45 2006 UTC revision 1688, Sat Dec 9 00:29:45 2006 UTC
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1    2006-12-08  Douglas Bates  <bates@stat.wisc.edu>
2    
3            * DESCRIPTION (Version): updated -> release 0.9975-7
4            * src/{init.c,chm_common.c}, inst/include/*: export cholmod_analyze_p
5    
6    2006-11-30  Martin Maechler  <maechler@stat.math.ethz.ch>
7    
8            * R/diagMatrix.R (%*%): write a direct [diag o Csparse] method
9    
10    2006-11-29  Douglas Bates  <bates@stat.wisc.edu>
11    
12            * src/dgeMatrix.c (dgeMatrix_solve): Check error code from dgetri.
13            * tests/dg_Matrix.R: Add Barry Rowlingson's test of a matrix that
14            is exactly singular.
15    
16    2006-11-07  Martin Maechler  <maechler@stat.math.ethz.ch>
17    
18            * DESCRIPTION (Date): updated -> release 0.9975-6
19    
20    2006-11-06  Martin Maechler  <maechler@stat.math.ethz.ch>
21    
22            * R/Csparse.R (replCmat): symmetric indexing of symmetric matrix
23            now returns symmetric.
24    
25            * R/zzz.R ("diag<-"): replace "diag<-" in base for R <= 2.4.x
26    
27            * R/Matrix.R (.M.sub.i.2col):  new, for  M[ cbind(i,j) ] indexing.
28            * R/Matrix.R (.M.repl.i.2col): new, for  M[ cbind(i,j) ] <- value
29    
30            * R/Auxiliaries.R (.type.kind): added
31    
32    2006-11-04  Martin Maechler  <maechler@stat.math.ethz.ch>
33    
34            * src/cs.[ch]: updated to CSparse Version 2.0.3 by simply
35            running src/CSparse_install.sh
36    
37            * R/denseMatrix.R: "[": keep symmetric on symmetric indexing.
38    
39    2006-11-03  Martin Maechler  <maechler@stat.math.ethz.ch>
40    
41            * src/dsCMatrix.c (dsCMatrix_Csparse_solve): new
42            * R/dsCMatrix.R (solve): "fully-sparse" using the above.
43    
44            * R/AllClass.R: "pMatrix" now also inherits from "generalMatrix"
45    
46            * tests/Class+Meth.R (tstMatrixClass): now assure
47            the (important in method programming) property :
48    
49                    ###>>  Every "Matrix" is either
50                    ###>>  "general*", "symmetric*", "triangular*" or "diagonal*"
51    
52                    (where "*" stands for "Matrix")
53    
54            * R/Auxiliaries.R (diagU2N): now .Call()s Csparse_diagU2N for <Csparse>
55    
56            * R/dMatrix.R (Compare(<dMatrix>,<dMatrix>): update and
57            * tests/validObj.R: checks for "comparison"
58    
59            * R/sparseMatrix.R ([): improved indexing for sparse;
60                    trying to keep <symmetric>[ n, n] symmmetric
61    
62            * tests/indexing.R: indexing for logical sparse now ok
63    
64    
65    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
66    
67            * src/Tsparse.c: use xTsparse_validate() , and hence remove
68    
69            * src/{ltC,lsC,lgT}Matrix.[ch]: removed
70    
71    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
72    
73            * R/AllClass.R (Matrix-class): check length of dimnames in validity.
74    
75            * tests/simple.R: validObject() checking the above.
76    
77            * src/dgCMatrix.c (xCMatrix_validate): new, small and simple,
78            replacing both dgCMatrix_validate and lgCM*.
79    
80            * src/Csparse.c (Csparse_dense_prod, etc): do not lose dimnames;
81            fix dimnames setting in other places.
82            * src/chm_common.c (chm_dense_to_SEXP): now can pass dimnames
83    
84    2006-11-01  Martin Maechler  <maechler@stat.math.ethz.ch>
85    
86            * R/Csparse.R,src/Csparse.c, etc: tcrossprod(<CsparseM>,<CsparseM>)
87    
88            * R/sparseMatrix.R (isSymmetric): drop 'factors' slot for
89            symmetry test, via
90            * R/Auxiliaries.R (.as.dgC.0.factors):
91    
92    2006-11-01  Douglas Bates  <bates@r-project.org>
93    
94            * R/Csparse.R,src/Csparse.c,tests/matprod.R,
95            man/CsparseMatrix-class.Rd: crossprod(<CsparseMatrix>,
96            <CsparseMatrix>) added
97    
98    2006-10-30  Martin Maechler  <maechler@stat.math.ethz.ch>
99    
100            * tests/matprod.R: add a variation of Harri's example
101    
102            * R/dsparseMatrix.R: fix crossprod(<dsparse>, <dge>) to *not*
103            recursive infinitely.
104    
105            * R/dgCMatrix.R: + solve(<sparse>, <sparse>)
106    
107            * tests/indexing.R: add test for the "<" bug fixed 10-27 in R/dMatrix.R
108    
109    2006-10-28  Martin Maechler  <maechler@stat.math.ethz.ch>
110    
111            * tests/Class+Meth.R (tstMatrixClass): more: use non-trivial
112            matrix if possible; test m+m == 2*m; now test dgRMatrix.
113            * R/dgRMatrix.R (.to.dgR): a few more coercions, in order to
114            satisfy the above test.
115    
116    2006-10-27  Martin Maechler  <maechler@stat.math.ethz.ch>
117    
118            * R/Matrix.R (Ops):  <Matrix> o <matrix>  method added
119    
120            * R/dgCMatrix.R: solve(a, b="missing") based on
121            * src/dgCMatrix.c (dgCMatrix_matrix_solve): extend to work with
122            RHS = NULL.
123    
124            * R/diagMatrix.R (diagdiagprod): extend %*% etc to ldiMatrix;
125            add more (needed) [t]crossprod() methods.
126    
127            * man/ddiMatrix-class.Rd: more info, notably on 'diag'
128    
129            * R/Auxiliaries.R (as_CspClass): cleanup
130            (drop0): internal utility for "Csparse_drop(*, 0)"
131            (.bail.out.2): encourage active feedback
132    
133    2006-10-26  Martin Maechler  <maechler@stat.math.ethz.ch>
134    
135            * R/dMatrix.R(Compare): new(), then slots [no validity check]
136    
137            * src/Csparse.c (Csparse_validate): fixed (and more efficient in
138            non-valid or 'sorted' case).
139    
140            * R/dsparseMatrix.R: add "chol" method.
141            * R/ddenseMatrix.R: ditto
142    
143            * R/diagMatrix.R (Ops): group methods for  <diagonal> o <sparse>
144            * NAMESPACE (Ops)
145            * R/diagMatrix.R (diag2T): simple utility used "higher level"
146            coercion; deprecating direct lower level coercions.
147    
148            * R/*.R (seq): use seq_len() and seq_along() where possible.
149    
150    
151    2006-10-23  Martin Maechler  <maechler@stat.math.ethz.ch>
152    
153            * DESCRIPTION (Version): 0.9975-5 ready for release
154    
155    2006-10-20  Douglas Bates  <bates@stat.wisc.edu>
156    
157            * src/init.c (R_init_Matrix): export more cholmod CCallable functions.
158    
159    2006-10-20  Martin Maechler  <maechler@stat.math.ethz.ch>
160    
161            * R/AllClass.R (corMatrix): add 'validity' check;
162                    comment out unused "LDL" class definition
163            * NAMESPACE: mention, but do not export "LDL" class
164            * R/corMatrix.R: new (simple), needed for R-devel with
165            * tests/Class+Meth.R (tstMatrixClass): 1 exception for corMatrix
166              coerce and t() exceptions for all 5 'Mat.MatFact' classes.
167    
168    2006-10-19  Douglas Bates  <bates@stat.wisc.edu>
169    
170            * src/chm_common.h: Add R_cholmod_start to initialize cholmod to
171            use Rprintf and R's error handling.
172    
173    2006-10-17  Martin Maechler  <maechler@stat.math.ethz.ch>
174    
175            * R/diagMatrix.R (%*%): rep(*, each = .) in Matrix %*% diagonal.
176            * tests/matprod.R: add tests for the bug fixed.
177    
178    2006-10-11  Douglas Bates  <bates@stat.wisc.edu>
179    
180            * src/HBMM.[ch]: remove HarwellBoeing format for writing.
181            * src/SOURCES_C.mkf (SOURCES_C): no longer compile iohb.c
182    
183    2006-10-06  Douglas Bates  <bates@stat.wisc.edu>
184    
185            * R/d[gs]CMatrix.R: deprecate the writeHB function.  Use writeMM instead.
186    
187    2006-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
188    
189            * DESCRIPTION (Version): 0.9975-3
190    
191            * R/diagMatrix.R (bdiag): new function constructing block diagonal
192            (sparse) matrices.
193            * man/bdiag.Rd: docu + examples
194    
195            * R/Csparse.R (replCmat): calling new Csparse_drop() now.
196    
197            * src/Csparse.c (Csparse_general_to_symmetric, Csparse_drop): new functions
198            * R/lsCMatrix.R: three more coercions to lsC (thanks to the above)
199    
200            * R/diagMatrix.R (Diagonal): '[<-' method for diag.matrices such
201            that result is sparse or diagonal (and not dense).
202    
203            * man/Subassign-methods.Rd: fix examples
204    
205            * R/Matrix.R (Matrix):  Matrix(0, *) or Matrix(*, sparse=TRUE)
206            should always return a sparse (and not sometimes a diagonal) matrix.
207    
208    2006-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
209    
210            * R/Matrix.R ([<-): also for value "Matrix" or "matrix"
211    
212    2006-10-04  Douglas Bates  <bates@stat.wisc.edu>
213    
214            * DESCRIPTION (Version): 0.9975-2
215    
216            * inst/include/Matrix_stubs.c (M_cholmod_sparse_to_triplet): export more symbols
217    
218    2006-10-02  Douglas Bates  <bates@R-project.org>
219    
220            * tests/dg_Matrix.R: Simplify test taking into account new code.
221    
222    2006-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
223    
224            * R/Csparse.R (replCmat): improve for missing i / j in non-simple cases
225    
226            * R/lsTMatrix.R: new files w/ missing methods
227            * R/nsTMatrix.R:  "  'for completeness'
228    
229            * tests/Class+Meth.R: a bit less 'not.ok.classes'
230    
231            * R/Tsparse.R (t): generalized "t" method from "dgT*" to "Tsparse*"
232    
233    
234    2006-09-28  Douglas Bates  <bates@R-project.org>
235    
236            * src/dppMatrix.h: Ensure definition of dspMatrix_validate is
237            included.
238    
239            * src/init.c, inst/include/{Matrix.h,Matrix_stubs.h,cholmod.h}:
240            Export C-callable functions used in Zt_create in lme4.
241    
242    2006-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
243    
244            * DESCRIPTION (Version): 0.9975-1
245    
246            * tests/simple.R: less checks fail; using NA, found that our
247                    kronecker() is not base-compatible with NA's.
248    
249            * R/dMatrix.R: "Compare" method now implemented for all cases
250    
251            * R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility
252    
253            * man/dtpMatrix-class.Rd: mention length of 'x' slot
254    
255            * src/dtpMatrix.c (dtpMatrix_validate): fix check
256            * src/dspMatrix.c (dspMatrix_validate): ditto
257    
258            * R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
259              including coercion to [nl]tTMatrix.
260    
261            * R/diagMatrix.R (show): print a header line as for other classes.
262    
263    2006-09-27  Martin Maechler  <maechler@stat.math.ethz.ch>
264    
265            * src/Makefile.win (SUBDIRS): fix typo
266    
267    2006-09-19  Martin Maechler  <maechler@stat.math.ethz.ch>
268    
269            * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
270    
271  2006-09-18  Douglas Bates  <bates@stat.wisc.edu>  2006-09-18  Douglas Bates  <bates@stat.wisc.edu>
272    
273          * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x          * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
# Line 54  Line 324 
324          * tests/: adaptions          * tests/: adaptions
325          * src/chm_common.c (chm_dense_to_SEXP): and others:          * src/chm_common.c (chm_dense_to_SEXP): and others:
326                  new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL                  new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
327          * src/Csparse.c, etc: dito          * src/Csparse.c, etc: ditto
328    
329  2006-09-11  Douglas Bates  <bates@R-project.org>  2006-09-11  Douglas Bates  <bates@R-project.org>
330    
# Line 73  Line 343 
343          * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()          * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
344    
345          * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"          * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
346          * man/tcrossprod.Rd: dito          * man/tcrossprod.Rd: ditto
347    
348  2006-09-08  Douglas Bates  <bates@stat.wisc.edu>  2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
349    
# Line 116  Line 386 
386    
387          * R/sparseMatrix.R (Arith): moved Arith group method one-level up          * R/sparseMatrix.R (Arith): moved Arith group method one-level up
388          from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"          from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
389          * R/dsparseMatrix.R: dito          * R/dsparseMatrix.R: ditto
390          * R/Csparse.R: dito          * R/Csparse.R: ditto
391    
392  2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
393    
# Line 133  Line 403 
403    
404          * 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
405          * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.          * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
406          (.is.diagonal): dito          (.is.diagonal): ditto
407    
408          * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's          * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
409    

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