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revision 1577, Mon Sep 18 21:01:45 2006 UTC revision 1696, Mon Dec 11 21:41:37 2006 UTC
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1    2006-12-11  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * R/Tsparse.R ([): fix long standing typo in symmetric case
4            * man/dsCMatrix-class.Rd: add example exhibiting the above case
5    
6    2006-12-10  Douglas Bates  <bates@stat.wisc.edu>
7    
8            * src/CHMfactor.c (CHMfactor_to_sparse): change LDL factorization
9            to LL before converting to a sparse matrix. (The LDL form can be
10            converted to a sparse matrix but it is implicitly a unit
11            triangular matrix and a diagonal matrix overwritten on the diagonal.)
12    
13    2006-12-09  Douglas Bates  <bates@stat.wisc.edu>
14    
15            * src/chm_common.c (chm_factor_to_SEXP): allocate and fill the Dim slot.
16    
17    2006-12-08  Douglas Bates  <bates@stat.wisc.edu>
18    
19            * DESCRIPTION (Version): updated -> release 0.9975-7
20            * src/{init.c,chm_common.c}, inst/include/*: export cholmod_analyze_p
21    
22    2006-11-30  Martin Maechler  <maechler@stat.math.ethz.ch>
23    
24            * R/diagMatrix.R (%*%): write a direct [diag o Csparse] method
25    
26    2006-11-29  Douglas Bates  <bates@stat.wisc.edu>
27    
28            * src/dgeMatrix.c (dgeMatrix_solve): Check error code from dgetri.
29            * tests/dg_Matrix.R: Add Barry Rowlingson's test of a matrix that
30            is exactly singular.
31    
32    2006-11-07  Martin Maechler  <maechler@stat.math.ethz.ch>
33    
34            * DESCRIPTION (Date): updated -> release 0.9975-6
35    
36    2006-11-06  Martin Maechler  <maechler@stat.math.ethz.ch>
37    
38            * R/Csparse.R (replCmat): symmetric indexing of symmetric matrix
39            now returns symmetric.
40    
41            * R/zzz.R ("diag<-"): replace "diag<-" in base for R <= 2.4.x
42    
43            * R/Matrix.R (.M.sub.i.2col):  new, for  M[ cbind(i,j) ] indexing.
44            * R/Matrix.R (.M.repl.i.2col): new, for  M[ cbind(i,j) ] <- value
45    
46            * R/Auxiliaries.R (.type.kind): added
47    
48    2006-11-04  Martin Maechler  <maechler@stat.math.ethz.ch>
49    
50            * src/cs.[ch]: updated to CSparse Version 2.0.3 by simply
51            running src/CSparse_install.sh
52    
53            * R/denseMatrix.R: "[": keep symmetric on symmetric indexing.
54    
55    2006-11-03  Martin Maechler  <maechler@stat.math.ethz.ch>
56    
57            * src/dsCMatrix.c (dsCMatrix_Csparse_solve): new
58            * R/dsCMatrix.R (solve): "fully-sparse" using the above.
59    
60            * R/AllClass.R: "pMatrix" now also inherits from "generalMatrix"
61    
62            * tests/Class+Meth.R (tstMatrixClass): now assure
63            the (important in method programming) property :
64    
65                    ###>>  Every "Matrix" is either
66                    ###>>  "general*", "symmetric*", "triangular*" or "diagonal*"
67    
68                    (where "*" stands for "Matrix")
69    
70            * R/Auxiliaries.R (diagU2N): now .Call()s Csparse_diagU2N for <Csparse>
71    
72            * R/dMatrix.R (Compare(<dMatrix>,<dMatrix>): update and
73            * tests/validObj.R: checks for "comparison"
74    
75            * R/sparseMatrix.R ([): improved indexing for sparse;
76                    trying to keep <symmetric>[ n, n] symmmetric
77    
78            * tests/indexing.R: indexing for logical sparse now ok
79    
80    
81    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
82    
83            * src/Tsparse.c: use xTsparse_validate() , and hence remove
84    
85            * src/{ltC,lsC,lgT}Matrix.[ch]: removed
86    
87    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
88    
89            * R/AllClass.R (Matrix-class): check length of dimnames in validity.
90    
91            * tests/simple.R: validObject() checking the above.
92    
93            * src/dgCMatrix.c (xCMatrix_validate): new, small and simple,
94            replacing both dgCMatrix_validate and lgCM*.
95    
96            * src/Csparse.c (Csparse_dense_prod, etc): do not lose dimnames;
97            fix dimnames setting in other places.
98            * src/chm_common.c (chm_dense_to_SEXP): now can pass dimnames
99    
100    2006-11-01  Martin Maechler  <maechler@stat.math.ethz.ch>
101    
102            * R/Csparse.R,src/Csparse.c, etc: tcrossprod(<CsparseM>,<CsparseM>)
103    
104            * R/sparseMatrix.R (isSymmetric): drop 'factors' slot for
105            symmetry test, via
106            * R/Auxiliaries.R (.as.dgC.0.factors):
107    
108    2006-11-01  Douglas Bates  <bates@r-project.org>
109    
110            * R/Csparse.R,src/Csparse.c,tests/matprod.R,
111            man/CsparseMatrix-class.Rd: crossprod(<CsparseMatrix>,
112            <CsparseMatrix>) added
113    
114    2006-10-30  Martin Maechler  <maechler@stat.math.ethz.ch>
115    
116            * tests/matprod.R: add a variation of Harri's example
117    
118            * R/dsparseMatrix.R: fix crossprod(<dsparse>, <dge>) to *not*
119            recursive infinitely.
120    
121            * R/dgCMatrix.R: + solve(<sparse>, <sparse>)
122    
123            * tests/indexing.R: add test for the "<" bug fixed 10-27 in R/dMatrix.R
124    
125    2006-10-28  Martin Maechler  <maechler@stat.math.ethz.ch>
126    
127            * tests/Class+Meth.R (tstMatrixClass): more: use non-trivial
128            matrix if possible; test m+m == 2*m; now test dgRMatrix.
129            * R/dgRMatrix.R (.to.dgR): a few more coercions, in order to
130            satisfy the above test.
131    
132    2006-10-27  Martin Maechler  <maechler@stat.math.ethz.ch>
133    
134            * R/Matrix.R (Ops):  <Matrix> o <matrix>  method added
135    
136            * R/dgCMatrix.R: solve(a, b="missing") based on
137            * src/dgCMatrix.c (dgCMatrix_matrix_solve): extend to work with
138            RHS = NULL.
139    
140            * R/diagMatrix.R (diagdiagprod): extend %*% etc to ldiMatrix;
141            add more (needed) [t]crossprod() methods.
142    
143            * man/ddiMatrix-class.Rd: more info, notably on 'diag'
144    
145            * R/Auxiliaries.R (as_CspClass): cleanup
146            (drop0): internal utility for "Csparse_drop(*, 0)"
147            (.bail.out.2): encourage active feedback
148    
149    2006-10-26  Martin Maechler  <maechler@stat.math.ethz.ch>
150    
151            * R/dMatrix.R(Compare): new(), then slots [no validity check]
152    
153            * src/Csparse.c (Csparse_validate): fixed (and more efficient in
154            non-valid or 'sorted' case).
155    
156            * R/dsparseMatrix.R: add "chol" method.
157            * R/ddenseMatrix.R: ditto
158    
159            * R/diagMatrix.R (Ops): group methods for  <diagonal> o <sparse>
160            * NAMESPACE (Ops)
161            * R/diagMatrix.R (diag2T): simple utility used "higher level"
162            coercion; deprecating direct lower level coercions.
163    
164            * R/*.R (seq): use seq_len() and seq_along() where possible.
165    
166    
167    2006-10-23  Martin Maechler  <maechler@stat.math.ethz.ch>
168    
169            * DESCRIPTION (Version): 0.9975-5 ready for release
170    
171    2006-10-20  Douglas Bates  <bates@stat.wisc.edu>
172    
173            * src/init.c (R_init_Matrix): export more cholmod CCallable functions.
174    
175    2006-10-20  Martin Maechler  <maechler@stat.math.ethz.ch>
176    
177            * R/AllClass.R (corMatrix): add 'validity' check;
178                    comment out unused "LDL" class definition
179            * NAMESPACE: mention, but do not export "LDL" class
180            * R/corMatrix.R: new (simple), needed for R-devel with
181            * tests/Class+Meth.R (tstMatrixClass): 1 exception for corMatrix
182              coerce and t() exceptions for all 5 'Mat.MatFact' classes.
183    
184    2006-10-19  Douglas Bates  <bates@stat.wisc.edu>
185    
186            * src/chm_common.h: Add R_cholmod_start to initialize cholmod to
187            use Rprintf and R's error handling.
188    
189    2006-10-17  Martin Maechler  <maechler@stat.math.ethz.ch>
190    
191            * R/diagMatrix.R (%*%): rep(*, each = .) in Matrix %*% diagonal.
192            * tests/matprod.R: add tests for the bug fixed.
193    
194    2006-10-11  Douglas Bates  <bates@stat.wisc.edu>
195    
196            * src/HBMM.[ch]: remove HarwellBoeing format for writing.
197            * src/SOURCES_C.mkf (SOURCES_C): no longer compile iohb.c
198    
199    2006-10-06  Douglas Bates  <bates@stat.wisc.edu>
200    
201            * R/d[gs]CMatrix.R: deprecate the writeHB function.  Use writeMM instead.
202    
203    2006-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
204    
205            * DESCRIPTION (Version): 0.9975-3
206    
207            * R/diagMatrix.R (bdiag): new function constructing block diagonal
208            (sparse) matrices.
209            * man/bdiag.Rd: docu + examples
210    
211            * R/Csparse.R (replCmat): calling new Csparse_drop() now.
212    
213            * src/Csparse.c (Csparse_general_to_symmetric, Csparse_drop): new functions
214            * R/lsCMatrix.R: three more coercions to lsC (thanks to the above)
215    
216            * R/diagMatrix.R (Diagonal): '[<-' method for diag.matrices such
217            that result is sparse or diagonal (and not dense).
218    
219            * man/Subassign-methods.Rd: fix examples
220    
221            * R/Matrix.R (Matrix):  Matrix(0, *) or Matrix(*, sparse=TRUE)
222            should always return a sparse (and not sometimes a diagonal) matrix.
223    
224    2006-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
225    
226            * R/Matrix.R ([<-): also for value "Matrix" or "matrix"
227    
228    2006-10-04  Douglas Bates  <bates@stat.wisc.edu>
229    
230            * DESCRIPTION (Version): 0.9975-2
231    
232            * inst/include/Matrix_stubs.c (M_cholmod_sparse_to_triplet): export more symbols
233    
234    2006-10-02  Douglas Bates  <bates@R-project.org>
235    
236            * tests/dg_Matrix.R: Simplify test taking into account new code.
237    
238    2006-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
239    
240            * R/Csparse.R (replCmat): improve for missing i / j in non-simple cases
241    
242            * R/lsTMatrix.R: new files w/ missing methods
243            * R/nsTMatrix.R:  "  'for completeness'
244    
245            * tests/Class+Meth.R: a bit less 'not.ok.classes'
246    
247            * R/Tsparse.R (t): generalized "t" method from "dgT*" to "Tsparse*"
248    
249    
250    2006-09-28  Douglas Bates  <bates@R-project.org>
251    
252            * src/dppMatrix.h: Ensure definition of dspMatrix_validate is
253            included.
254    
255            * src/init.c, inst/include/{Matrix.h,Matrix_stubs.h,cholmod.h}:
256            Export C-callable functions used in Zt_create in lme4.
257    
258    2006-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
259    
260            * DESCRIPTION (Version): 0.9975-1
261    
262            * tests/simple.R: less checks fail; using NA, found that our
263                    kronecker() is not base-compatible with NA's.
264    
265            * R/dMatrix.R: "Compare" method now implemented for all cases
266    
267            * R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility
268    
269            * man/dtpMatrix-class.Rd: mention length of 'x' slot
270    
271            * src/dtpMatrix.c (dtpMatrix_validate): fix check
272            * src/dspMatrix.c (dspMatrix_validate): ditto
273    
274            * R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
275              including coercion to [nl]tTMatrix.
276    
277            * R/diagMatrix.R (show): print a header line as for other classes.
278    
279    2006-09-27  Martin Maechler  <maechler@stat.math.ethz.ch>
280    
281            * src/Makefile.win (SUBDIRS): fix typo
282    
283    2006-09-19  Martin Maechler  <maechler@stat.math.ethz.ch>
284    
285            * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
286    
287  2006-09-18  Douglas Bates  <bates@stat.wisc.edu>  2006-09-18  Douglas Bates  <bates@stat.wisc.edu>
288    
289          * 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 340 
340          * tests/: adaptions          * tests/: adaptions
341          * src/chm_common.c (chm_dense_to_SEXP): and others:          * src/chm_common.c (chm_dense_to_SEXP): and others:
342                  new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL                  new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
343          * src/Csparse.c, etc: dito          * src/Csparse.c, etc: ditto
344    
345  2006-09-11  Douglas Bates  <bates@R-project.org>  2006-09-11  Douglas Bates  <bates@R-project.org>
346    
# Line 73  Line 359 
359          * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()          * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
360    
361          * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"          * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
362          * man/tcrossprod.Rd: dito          * man/tcrossprod.Rd: ditto
363    
364  2006-09-08  Douglas Bates  <bates@stat.wisc.edu>  2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
365    
# Line 116  Line 402 
402    
403          * R/sparseMatrix.R (Arith): moved Arith group method one-level up          * R/sparseMatrix.R (Arith): moved Arith group method one-level up
404          from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"          from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
405          * R/dsparseMatrix.R: dito          * R/dsparseMatrix.R: ditto
406          * R/Csparse.R: dito          * R/Csparse.R: ditto
407    
408  2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
409    
# Line 133  Line 419 
419    
420          * 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
421          * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.          * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
422          (.is.diagonal): dito          (.is.diagonal): ditto
423    
424          * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's          * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
425    

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