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revision 1507, Mon Sep 4 18:41:34 2006 UTC revision 1674, Tue Nov 7 13:29:23 2006 UTC
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1    2006-11-07  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * DESCRIPTION (Date): updated -> release 0.9975-6
4    
5    2006-11-06  Martin Maechler  <maechler@stat.math.ethz.ch>
6    
7            * R/Csparse.R (replCmat): symmetric indexing of symmetric matrix
8            now returns symmetric.
9    
10            * R/zzz.R ("diag<-"): replace "diag<-" in base for R <= 2.4.x
11    
12            * R/Matrix.R (.M.sub.i.2col):  new, for  M[ cbind(i,j) ] indexing.
13            * R/Matrix.R (.M.repl.i.2col): new, for  M[ cbind(i,j) ] <- value
14    
15            * R/Auxiliaries.R (.type.kind): added
16    
17    2006-11-04  Martin Maechler  <maechler@stat.math.ethz.ch>
18    
19            * src/cs.[ch]: updated to CSparse Version 2.0.3 by simply
20            running src/CSparse_install.sh
21    
22            * R/denseMatrix.R: "[": keep symmetric on symmetric indexing.
23    
24    2006-11-03  Martin Maechler  <maechler@stat.math.ethz.ch>
25    
26            * src/dsCMatrix.c (dsCMatrix_Csparse_solve): new
27            * R/dsCMatrix.R (solve): "fully-sparse" using the above.
28    
29            * R/AllClass.R: "pMatrix" now also inherits from "generalMatrix"
30    
31            * tests/Class+Meth.R (tstMatrixClass): now assure
32            the (important in method programming) property :
33    
34                    ###>>  Every "Matrix" is either
35                    ###>>  "general*", "symmetric*", "triangular*" or "diagonal*"
36    
37                    (where "*" stands for "Matrix")
38    
39            * R/Auxiliaries.R (diagU2N): now .Call()s Csparse_diagU2N for <Csparse>
40    
41            * R/dMatrix.R (Compare(<dMatrix>,<dMatrix>): update and
42            * tests/validObj.R: checks for "comparison"
43    
44            * R/sparseMatrix.R ([): improved indexing for sparse;
45                    trying to keep <symmetric>[ n, n] symmmetric
46    
47            * tests/indexing.R: indexing for logical sparse now ok
48    
49    
50    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
51    
52            * src/Tsparse.c: use xTsparse_validate() , and hence remove
53    
54            * src/{ltC,lsC,lgT}Matrix.[ch]: removed
55    
56    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
57    
58            * R/AllClass.R (Matrix-class): check length of dimnames in validity.
59    
60            * tests/simple.R: validObject() checking the above.
61    
62            * src/dgCMatrix.c (xCMatrix_validate): new, small and simple,
63            replacing both dgCMatrix_validate and lgCM*.
64    
65            * src/Csparse.c (Csparse_dense_prod, etc): do not lose dimnames;
66            fix dimnames setting in other places.
67            * src/chm_common.c (chm_dense_to_SEXP): now can pass dimnames
68    
69    2006-11-01  Martin Maechler  <maechler@stat.math.ethz.ch>
70    
71            * R/Csparse.R,src/Csparse.c, etc: tcrossprod(<CsparseM>,<CsparseM>)
72    
73            * R/sparseMatrix.R (isSymmetric): drop 'factors' slot for
74            symmetry test, via
75            * R/Auxiliaries.R (.as.dgC.0.factors):
76    
77    2006-11-01  Douglas Bates  <bates@r-project.org>
78    
79            * R/Csparse.R,src/Csparse.c,tests/matprod.R,
80            man/CsparseMatrix-class.Rd: crossprod(<CsparseMatrix>,
81            <CsparseMatrix>) added
82    
83    2006-10-30  Martin Maechler  <maechler@stat.math.ethz.ch>
84    
85            * tests/matprod.R: add a variation of Harri's example
86    
87            * R/dsparseMatrix.R: fix crossprod(<dsparse>, <dge>) to *not*
88            recursive infinitely.
89    
90            * R/dgCMatrix.R: + solve(<sparse>, <sparse>)
91    
92            * tests/indexing.R: add test for the "<" bug fixed 10-27 in R/dMatrix.R
93    
94    2006-10-28  Martin Maechler  <maechler@stat.math.ethz.ch>
95    
96            * tests/Class+Meth.R (tstMatrixClass): more: use non-trivial
97            matrix if possible; test m+m == 2*m; now test dgRMatrix.
98            * R/dgRMatrix.R (.to.dgR): a few more coercions, in order to
99            satisfy the above test.
100    
101    2006-10-27  Martin Maechler  <maechler@stat.math.ethz.ch>
102    
103            * R/Matrix.R (Ops):  <Matrix> o <matrix>  method added
104    
105            * R/dgCMatrix.R: solve(a, b="missing") based on
106            * src/dgCMatrix.c (dgCMatrix_matrix_solve): extend to work with
107            RHS = NULL.
108    
109            * R/diagMatrix.R (diagdiagprod): extend %*% etc to ldiMatrix;
110            add more (needed) [t]crossprod() methods.
111    
112            * man/ddiMatrix-class.Rd: more info, notably on 'diag'
113    
114            * R/Auxiliaries.R (as_CspClass): cleanup
115            (drop0): internal utility for "Csparse_drop(*, 0)"
116            (.bail.out.2): encourage active feedback
117    
118    2006-10-26  Martin Maechler  <maechler@stat.math.ethz.ch>
119    
120            * R/dMatrix.R(Compare): new(), then slots [no validity check]
121    
122            * src/Csparse.c (Csparse_validate): fixed (and more efficient in
123            non-valid or 'sorted' case).
124    
125            * R/dsparseMatrix.R: add "chol" method.
126            * R/ddenseMatrix.R: ditto
127    
128            * R/diagMatrix.R (Ops): group methods for  <diagonal> o <sparse>
129            * NAMESPACE (Ops)
130            * R/diagMatrix.R (diag2T): simple utility used "higher level"
131            coercion; deprecating direct lower level coercions.
132    
133            * R/*.R (seq): use seq_len() and seq_along() where possible.
134    
135    
136    2006-10-23  Martin Maechler  <maechler@stat.math.ethz.ch>
137    
138            * DESCRIPTION (Version): 0.9975-5 ready for release
139    
140    2006-10-20  Douglas Bates  <bates@stat.wisc.edu>
141    
142            * src/init.c (R_init_Matrix): export more cholmod CCallable functions.
143    
144    2006-10-20  Martin Maechler  <maechler@stat.math.ethz.ch>
145    
146            * R/AllClass.R (corMatrix): add 'validity' check;
147                    comment out unused "LDL" class definition
148            * NAMESPACE: mention, but do not export "LDL" class
149            * R/corMatrix.R: new (simple), needed for R-devel with
150            * tests/Class+Meth.R (tstMatrixClass): 1 exception for corMatrix
151              coerce and t() exceptions for all 5 'Mat.MatFact' classes.
152    
153    2006-10-19  Douglas Bates  <bates@stat.wisc.edu>
154    
155            * src/chm_common.h: Add R_cholmod_start to initialize cholmod to
156            use Rprintf and R's error handling.
157    
158    2006-10-17  Martin Maechler  <maechler@stat.math.ethz.ch>
159    
160            * R/diagMatrix.R (%*%): rep(*, each = .) in Matrix %*% diagonal.
161            * tests/matprod.R: add tests for the bug fixed.
162    
163    2006-10-11  Douglas Bates  <bates@stat.wisc.edu>
164    
165            * src/HBMM.[ch]: remove HarwellBoeing format for writing.
166            * src/SOURCES_C.mkf (SOURCES_C): no longer compile iohb.c
167    
168    2006-10-06  Douglas Bates  <bates@stat.wisc.edu>
169    
170            * R/d[gs]CMatrix.R: deprecate the writeHB function.  Use writeMM instead.
171    
172    2006-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
173    
174            * DESCRIPTION (Version): 0.9975-3
175    
176            * R/diagMatrix.R (bdiag): new function constructing block diagonal
177            (sparse) matrices.
178            * man/bdiag.Rd: docu + examples
179    
180            * R/Csparse.R (replCmat): calling new Csparse_drop() now.
181    
182            * src/Csparse.c (Csparse_general_to_symmetric, Csparse_drop): new functions
183            * R/lsCMatrix.R: three more coercions to lsC (thanks to the above)
184    
185            * R/diagMatrix.R (Diagonal): '[<-' method for diag.matrices such
186            that result is sparse or diagonal (and not dense).
187    
188            * man/Subassign-methods.Rd: fix examples
189    
190            * R/Matrix.R (Matrix):  Matrix(0, *) or Matrix(*, sparse=TRUE)
191            should always return a sparse (and not sometimes a diagonal) matrix.
192    
193    2006-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
194    
195            * R/Matrix.R ([<-): also for value "Matrix" or "matrix"
196    
197    2006-10-04  Douglas Bates  <bates@stat.wisc.edu>
198    
199            * DESCRIPTION (Version): 0.9975-2
200    
201            * inst/include/Matrix_stubs.c (M_cholmod_sparse_to_triplet): export more symbols
202    
203    2006-10-02  Douglas Bates  <bates@R-project.org>
204    
205            * tests/dg_Matrix.R: Simplify test taking into account new code.
206    
207    2006-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
208    
209            * R/Csparse.R (replCmat): improve for missing i / j in non-simple cases
210    
211            * R/lsTMatrix.R: new files w/ missing methods
212            * R/nsTMatrix.R:  "  'for completeness'
213    
214            * tests/Class+Meth.R: a bit less 'not.ok.classes'
215    
216            * R/Tsparse.R (t): generalized "t" method from "dgT*" to "Tsparse*"
217    
218    
219    2006-09-28  Douglas Bates  <bates@R-project.org>
220    
221            * src/dppMatrix.h: Ensure definition of dspMatrix_validate is
222            included.
223    
224            * src/init.c, inst/include/{Matrix.h,Matrix_stubs.h,cholmod.h}:
225            Export C-callable functions used in Zt_create in lme4.
226    
227    2006-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
228    
229            * DESCRIPTION (Version): 0.9975-1
230    
231            * tests/simple.R: less checks fail; using NA, found that our
232                    kronecker() is not base-compatible with NA's.
233    
234            * R/dMatrix.R: "Compare" method now implemented for all cases
235    
236            * R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility
237    
238            * man/dtpMatrix-class.Rd: mention length of 'x' slot
239    
240            * src/dtpMatrix.c (dtpMatrix_validate): fix check
241            * src/dspMatrix.c (dspMatrix_validate): ditto
242    
243            * R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
244              including coercion to [nl]tTMatrix.
245    
246            * R/diagMatrix.R (show): print a header line as for other classes.
247    
248    2006-09-27  Martin Maechler  <maechler@stat.math.ethz.ch>
249    
250            * src/Makefile.win (SUBDIRS): fix typo
251    
252    2006-09-19  Martin Maechler  <maechler@stat.math.ethz.ch>
253    
254            * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
255    
256    2006-09-18  Douglas Bates  <bates@stat.wisc.edu>
257    
258            * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
259            symmetric and y missing in R code using %*% (cholmod_aat doesn't
260            accept a symmetric matrix).
261            * tests/group-methods.R: Uncomment test of crossprod applied to
262            lsCMatrix objects.
263    
264    2006-09-18  Martin Maechler  <maechler@stat.math.ethz.ch>
265    
266            * R/AllClass.R (symmetricMatrix): add validity method (available
267            in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
268    
269            * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
270    
271            * tests/indexing.Rout.save:
272            * tests/indexing.R: additions, mainly for 'lsparse'
273    
274            * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
275            case.
276    
277            * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
278    
279    2006-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
280    
281            * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
282                    as 'N' (1-letter - Ok?)
283    
284            * tests/group-methods.R: add test for logical + NAs
285    
286            * R/dMatrix.R ("Compare"): fix to work with NA's
287    
288            * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
289    
290            * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
291                    which is implemented.
292    
293    2006-09-15  Martin Maechler  <maechler@stat.math.ethz.ch>
294    
295            * src/chm_common.c: coerce logical <-> double instead of
296            typecasting;  needed for "l" matrix handling in cholmod.
297    
298            * tests/other-pkgs.R (graph): small extension in "graph" checks.
299    
300            * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
301            (Tsp2grNEL): other fixes needed
302    
303    2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
304    
305            * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
306                    Matrices, since "lMatrix", also "lsparseM" can have NA
307            * R/ndenseMatrix.R, etc: new source files
308            * man/nsparseMatrix-classes.Rd, etc: new help files
309            * tests/: adaptions
310            * src/chm_common.c (chm_dense_to_SEXP): and others:
311                    new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
312            * src/Csparse.c, etc: ditto
313    
314    2006-09-11  Douglas Bates  <bates@R-project.org>
315    
316            * src/Mutils.[ch],init.c inst/include/*.h: Move the
317            alloc_d**Matrix functions to the lme4 package.
318    
319    2006-09-09  Douglas Bates  <bates@R-project.org>
320    
321            * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
322            fixed
323    
324    2006-09-09  Martin Maechler  <maechler@stat.math.ethz.ch>
325    
326            * R/lMatrix.R: new
327    
328            * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
329    
330            * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
331            * man/tcrossprod.Rd: ditto
332    
333    2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
334    
335            * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
336            for exported functions
337            * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
338            Remove partitioning algorithms for sparse matrix reordering.  The
339            copyright on the Metis code was problematic and the methods were
340            rarely used.
341            * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
342            operations are now done entirely in CHOLMOD code.
343    
344    2006-09-06  Douglas Bates  <bates@R-project.org>
345    
346            * src/Mutils.h: Remove functions that are no longer used.
347    
348  2006-09-04  Douglas Bates  <bates@R-project.org>  2006-09-04  Douglas Bates  <bates@R-project.org>
349    
350          * src/dtCMatrix.c (dtCMatrix_validate): rename functions.          * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
# Line 24  Line 371 
371    
372          * R/sparseMatrix.R (Arith): moved Arith group method one-level up          * R/sparseMatrix.R (Arith): moved Arith group method one-level up
373          from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"          from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
374          * R/dsparseMatrix.R: dito          * R/dsparseMatrix.R: ditto
375          * R/Csparse.R: dito          * R/Csparse.R: ditto
376    
377  2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
378    
# Line 41  Line 388 
388    
389          * 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
390          * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.          * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
391          (.is.diagonal): dito          (.is.diagonal): ditto
392    
393          * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's          * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
394    

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