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revision 1548, Mon Sep 11 22:13:07 2006 UTC revision 1714, Thu Dec 28 22:11:32 2006 UTC
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1    2006-12-28  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * R/Ops.R ("Arith" etc): move almost all "Ops" methods to new R
4            file; start using "Logic", hence
5    
6            * DESCRIPTION (Depends): R >= 2.4.1 (since we want "Logic")
7            * NAMESPACE: import and export "Logic"
8    
9    2006-12-27  Martin Maechler  <maechler@stat.math.ethz.ch>
10    
11            * src/zpotfr.f and dependencies: use LAPACK 3.1 version
12            only needed previously to R version 2.5.0.
13    
14    2006-12-26  Martin Maechler  <maechler@stat.math.ethz.ch>
15    
16            * DESCRIPTION (Date, Version): 0.9975-8, ready for release
17    
18            * R/Tsparse.R (replTmat): fix subassignment of triangular
19            * R/Csparse.R (replCmat): ditto
20            * tests/indexing.R: more tests, incl the above fix
21    
22    2006-12-23  Martin Maechler  <maechler@stat.math.ethz.ch>
23    
24            * R/Auxiliaries.R (drop0): extend for non CSparse
25            * R/Auxiliaries.R (diagU2N): should work for all sparseMatrix
26    
27            * src/Csparse.c (Csparse_to_Tsparse, Csparse_general_to_symmetric):
28                    use uplo correctly (!); other places: use uplo_P() macro
29    
30            * R/Csparse.R (replCmat): call diagU2N() when needed
31            * R/Tsparse.R (replTmat): ditto
32    
33            * src/dtCMatrix.c (tCMatrix_validate): new
34            * src/dtTMatrix.c (tTMatrix_validate): new, used in
35            * R/AllClass.R: for validity of dtC, dsC, and dtT, dsT.
36    
37            * R/diagMatrix.R (replDiag): to use in [<-
38    
39    2006-12-22  Martin Maechler  <maechler@stat.math.ethz.ch>
40    
41            * R/Auxiliaries.R (as_Csparse2, as_geSimpl): new functions;
42                    also more general diagU2N().
43    
44    2006-12-21  Martin Maechler  <maechler@stat.math.ethz.ch>
45    
46            * R/bind2.R: new file for all cbind2(), rbind() methods moved here
47            from R/<foo>Matrix.R files. Better diagonal & improved sparse methods.
48    
49    2006-12-20  Martin Maechler  <maechler@stat.math.ethz.ch>
50    
51            * tests/bind.R: a few more cases
52            * R/Auxiliaries.R (.M.kind): also work for atomic vectors
53    
54            * R/denseMatrix.R (cbind2/rbind2): moved here (and generalized) from
55            * R/ddenseMatrix.R (cbind2/rbind2)
56            * R/Tsparse.R (replTmat): final(?!) fix for "[<-" ..
57            * tests/indexing.R
58            * tests/indexing.Rout.save: updated
59    
60    2006-12-18  Martin Maechler  <maechler@stat.math.ethz.ch>
61    
62            * R/Tsparse.R (replTmat): fixed a remaining "[<-" bug in
63            * tests/indexing.R
64    
65    2006-12-15  Martin Maechler  <maechler@stat.math.ethz.ch>
66    
67            * R/sparseMatrix.R (prSpMatrix): "." alignment much improved:
68            align with proper position of "0", i.e., right for integers.
69            argument 'align' by default is "fancy".
70    
71    2006-12-14  Martin Maechler  <maechler@stat.math.ethz.ch>
72    
73            * R/sparseMatrix.R: delegate "Compare" to "Csparse.."
74            * R/Csparse.R: and fix "Compare" for more cases.
75            * tests/Class+Meth.R: test some of these (m == m, m != m)
76    
77    2006-12-13  Martin Maechler  <maechler@stat.math.ethz.ch>
78    
79            * R/lsparseMatrix.R: all() and any() methods
80            * R/ldenseMatrix.R:      ditto
81            * NAMESPACE, R/Matrix.R: ditto
82    
83            * man/all-methods.Rd: document them minimally
84    
85            * tests/simple.R: add a few examples for these
86    
87    2006-12-11  Martin Maechler  <maechler@stat.math.ethz.ch>
88    
89            * R/Tsparse.R ([): fix long standing typo in symmetric case
90            * man/dsCMatrix-class.Rd: add example exhibiting the above case
91    
92    2006-12-10  Douglas Bates  <bates@stat.wisc.edu>
93    
94            * src/CHMfactor.c (CHMfactor_to_sparse): change LDL factorization
95            to LL before converting to a sparse matrix. (The LDL form can be
96            converted to a sparse matrix but it is implicitly a unit
97            triangular matrix and a diagonal matrix overwritten on the diagonal.)
98    
99    2006-12-09  Douglas Bates  <bates@stat.wisc.edu>
100    
101            * src/chm_common.c (chm_factor_to_SEXP): allocate and fill the Dim slot.
102    
103    2006-12-08  Douglas Bates  <bates@stat.wisc.edu>
104    
105            * DESCRIPTION (Version): updated -> release 0.9975-7
106            * src/{init.c,chm_common.c}, inst/include/*: export cholmod_analyze_p
107    
108    2006-11-30  Martin Maechler  <maechler@stat.math.ethz.ch>
109    
110            * R/diagMatrix.R (%*%): write a direct [diag o Csparse] method
111    
112    2006-11-29  Douglas Bates  <bates@stat.wisc.edu>
113    
114            * src/dgeMatrix.c (dgeMatrix_solve): Check error code from dgetri.
115            * tests/dg_Matrix.R: Add Barry Rowlingson's test of a matrix that
116            is exactly singular.
117    
118    2006-11-07  Martin Maechler  <maechler@stat.math.ethz.ch>
119    
120            * DESCRIPTION (Date): updated -> release 0.9975-6
121    
122    2006-11-06  Martin Maechler  <maechler@stat.math.ethz.ch>
123    
124            * R/Csparse.R (replCmat): symmetric indexing of symmetric matrix
125            now returns symmetric.
126    
127            * R/zzz.R ("diag<-"): replace "diag<-" in base for R <= 2.4.x
128    
129            * R/Matrix.R (.M.sub.i.2col):  new, for  M[ cbind(i,j) ] indexing.
130            * R/Matrix.R (.M.repl.i.2col): new, for  M[ cbind(i,j) ] <- value
131    
132            * R/Auxiliaries.R (.type.kind): added
133    
134    2006-11-04  Martin Maechler  <maechler@stat.math.ethz.ch>
135    
136            * src/cs.[ch]: updated to CSparse Version 2.0.3 by simply
137            running src/CSparse_install.sh
138    
139            * R/denseMatrix.R: "[": keep symmetric on symmetric indexing.
140    
141    2006-11-03  Martin Maechler  <maechler@stat.math.ethz.ch>
142    
143            * src/dsCMatrix.c (dsCMatrix_Csparse_solve): new
144            * R/dsCMatrix.R (solve): "fully-sparse" using the above.
145    
146            * R/AllClass.R: "pMatrix" now also inherits from "generalMatrix"
147    
148            * tests/Class+Meth.R (tstMatrixClass): now assure
149            the (important in method programming) property :
150    
151                    ###>>  Every "Matrix" is either
152                    ###>>  "general*", "symmetric*", "triangular*" or "diagonal*"
153    
154                    (where "*" stands for "Matrix")
155    
156            * R/Auxiliaries.R (diagU2N): now .Call()s Csparse_diagU2N for <Csparse>
157    
158            * R/dMatrix.R (Compare(<dMatrix>,<dMatrix>): update and
159            * tests/validObj.R: checks for "comparison"
160    
161            * R/sparseMatrix.R ([): improved indexing for sparse;
162                    trying to keep <symmetric>[ n, n] symmmetric
163    
164            * tests/indexing.R: indexing for logical sparse now ok
165    
166    
167    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
168    
169            * src/Tsparse.c: use xTsparse_validate() , and hence remove
170    
171            * src/{ltC,lsC,lgT}Matrix.[ch]: removed
172    
173    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
174    
175            * R/AllClass.R (Matrix-class): check length of dimnames in validity.
176    
177            * tests/simple.R: validObject() checking the above.
178    
179            * src/dgCMatrix.c (xCMatrix_validate): new, small and simple,
180            replacing both dgCMatrix_validate and lgCM*.
181    
182            * src/Csparse.c (Csparse_dense_prod, etc): do not lose dimnames;
183            fix dimnames setting in other places.
184            * src/chm_common.c (chm_dense_to_SEXP): now can pass dimnames
185    
186    2006-11-01  Martin Maechler  <maechler@stat.math.ethz.ch>
187    
188            * R/Csparse.R,src/Csparse.c, etc: tcrossprod(<CsparseM>,<CsparseM>)
189    
190            * R/sparseMatrix.R (isSymmetric): drop 'factors' slot for
191            symmetry test, via
192            * R/Auxiliaries.R (.as.dgC.0.factors):
193    
194    2006-11-01  Douglas Bates  <bates@r-project.org>
195    
196            * R/Csparse.R,src/Csparse.c,tests/matprod.R,
197            man/CsparseMatrix-class.Rd: crossprod(<CsparseMatrix>,
198            <CsparseMatrix>) added
199    
200    2006-10-30  Martin Maechler  <maechler@stat.math.ethz.ch>
201    
202            * tests/matprod.R: add a variation of Harri's example
203    
204            * R/dsparseMatrix.R: fix crossprod(<dsparse>, <dge>) to *not*
205            recursive infinitely.
206    
207            * R/dgCMatrix.R: + solve(<sparse>, <sparse>)
208    
209            * tests/indexing.R: add test for the "<" bug fixed 10-27 in R/dMatrix.R
210    
211    2006-10-28  Martin Maechler  <maechler@stat.math.ethz.ch>
212    
213            * tests/Class+Meth.R (tstMatrixClass): more: use non-trivial
214            matrix if possible; test m+m == 2*m; now test dgRMatrix.
215            * R/dgRMatrix.R (.to.dgR): a few more coercions, in order to
216            satisfy the above test.
217    
218    2006-10-27  Martin Maechler  <maechler@stat.math.ethz.ch>
219    
220            * R/Matrix.R (Ops):  <Matrix> o <matrix>  method added
221    
222            * R/dgCMatrix.R: solve(a, b="missing") based on
223            * src/dgCMatrix.c (dgCMatrix_matrix_solve): extend to work with
224            RHS = NULL.
225    
226            * R/diagMatrix.R (diagdiagprod): extend %*% etc to ldiMatrix;
227            add more (needed) [t]crossprod() methods.
228    
229            * man/ddiMatrix-class.Rd: more info, notably on 'diag'
230    
231            * R/Auxiliaries.R (as_CspClass): cleanup
232            (drop0): internal utility for "Csparse_drop(*, 0)"
233            (.bail.out.2): encourage active feedback
234    
235    2006-10-26  Martin Maechler  <maechler@stat.math.ethz.ch>
236    
237            * R/dMatrix.R(Compare): new(), then slots [no validity check]
238    
239            * src/Csparse.c (Csparse_validate): fixed (and more efficient in
240            non-valid or 'sorted' case).
241    
242            * R/dsparseMatrix.R: add "chol" method.
243            * R/ddenseMatrix.R: ditto
244    
245            * R/diagMatrix.R (Ops): group methods for  <diagonal> o <sparse>
246            * NAMESPACE (Ops)
247            * R/diagMatrix.R (diag2T): simple utility used "higher level"
248            coercion; deprecating direct lower level coercions.
249    
250            * R/*.R (seq): use seq_len() and seq_along() where possible.
251    
252    
253    2006-10-23  Martin Maechler  <maechler@stat.math.ethz.ch>
254    
255            * DESCRIPTION (Version): 0.9975-5 ready for release
256    
257    2006-10-20  Douglas Bates  <bates@stat.wisc.edu>
258    
259            * src/init.c (R_init_Matrix): export more cholmod CCallable functions.
260    
261    2006-10-20  Martin Maechler  <maechler@stat.math.ethz.ch>
262    
263            * R/AllClass.R (corMatrix): add 'validity' check;
264                    comment out unused "LDL" class definition
265            * NAMESPACE: mention, but do not export "LDL" class
266            * R/corMatrix.R: new (simple), needed for R-devel with
267            * tests/Class+Meth.R (tstMatrixClass): 1 exception for corMatrix
268              coerce and t() exceptions for all 5 'Mat.MatFact' classes.
269    
270    2006-10-19  Douglas Bates  <bates@stat.wisc.edu>
271    
272            * src/chm_common.h: Add R_cholmod_start to initialize cholmod to
273            use Rprintf and R's error handling.
274    
275    2006-10-17  Martin Maechler  <maechler@stat.math.ethz.ch>
276    
277            * R/diagMatrix.R (%*%): rep(*, each = .) in Matrix %*% diagonal.
278            * tests/matprod.R: add tests for the bug fixed.
279    
280    2006-10-11  Douglas Bates  <bates@stat.wisc.edu>
281    
282            * src/HBMM.[ch]: remove HarwellBoeing format for writing.
283            * src/SOURCES_C.mkf (SOURCES_C): no longer compile iohb.c
284    
285    2006-10-06  Douglas Bates  <bates@stat.wisc.edu>
286    
287            * R/d[gs]CMatrix.R: deprecate the writeHB function.  Use writeMM instead.
288    
289    2006-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
290    
291            * DESCRIPTION (Version): 0.9975-3
292    
293            * R/diagMatrix.R (bdiag): new function constructing block diagonal
294            (sparse) matrices.
295            * man/bdiag.Rd: docu + examples
296    
297            * R/Csparse.R (replCmat): calling new Csparse_drop() now.
298    
299            * src/Csparse.c (Csparse_general_to_symmetric, Csparse_drop): new functions
300            * R/lsCMatrix.R: three more coercions to lsC (thanks to the above)
301    
302            * R/diagMatrix.R (Diagonal): '[<-' method for diag.matrices such
303            that result is sparse or diagonal (and not dense).
304    
305            * man/Subassign-methods.Rd: fix examples
306    
307            * R/Matrix.R (Matrix):  Matrix(0, *) or Matrix(*, sparse=TRUE)
308            should always return a sparse (and not sometimes a diagonal) matrix.
309    
310    2006-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
311    
312            * R/Matrix.R ([<-): also for value "Matrix" or "matrix"
313    
314    2006-10-04  Douglas Bates  <bates@stat.wisc.edu>
315    
316            * DESCRIPTION (Version): 0.9975-2
317    
318            * inst/include/Matrix_stubs.c (M_cholmod_sparse_to_triplet): export more symbols
319    
320    2006-10-02  Douglas Bates  <bates@R-project.org>
321    
322            * tests/dg_Matrix.R: Simplify test taking into account new code.
323    
324    2006-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
325    
326            * R/Csparse.R (replCmat): improve for missing i / j in non-simple cases
327    
328            * R/lsTMatrix.R: new files w/ missing methods
329            * R/nsTMatrix.R:  "  'for completeness'
330    
331            * tests/Class+Meth.R: a bit less 'not.ok.classes'
332    
333            * R/Tsparse.R (t): generalized "t" method from "dgT*" to "Tsparse*"
334    
335    
336    2006-09-28  Douglas Bates  <bates@R-project.org>
337    
338            * src/dppMatrix.h: Ensure definition of dspMatrix_validate is
339            included.
340    
341            * src/init.c, inst/include/{Matrix.h,Matrix_stubs.h,cholmod.h}:
342            Export C-callable functions used in Zt_create in lme4.
343    
344    2006-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
345    
346            * DESCRIPTION (Version): 0.9975-1
347    
348            * tests/simple.R: less checks fail; using NA, found that our
349                    kronecker() is not base-compatible with NA's.
350    
351            * R/dMatrix.R: "Compare" method now implemented for all cases
352    
353            * R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility
354    
355            * man/dtpMatrix-class.Rd: mention length of 'x' slot
356    
357            * src/dtpMatrix.c (dtpMatrix_validate): fix check
358            * src/dspMatrix.c (dspMatrix_validate): ditto
359    
360            * R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
361              including coercion to [nl]tTMatrix.
362    
363            * R/diagMatrix.R (show): print a header line as for other classes.
364    
365    2006-09-27  Martin Maechler  <maechler@stat.math.ethz.ch>
366    
367            * src/Makefile.win (SUBDIRS): fix typo
368    
369    2006-09-19  Martin Maechler  <maechler@stat.math.ethz.ch>
370    
371            * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
372    
373    2006-09-18  Douglas Bates  <bates@stat.wisc.edu>
374    
375            * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
376            symmetric and y missing in R code using %*% (cholmod_aat doesn't
377            accept a symmetric matrix).
378            * tests/group-methods.R: Uncomment test of crossprod applied to
379            lsCMatrix objects.
380    
381    2006-09-18  Martin Maechler  <maechler@stat.math.ethz.ch>
382    
383            * R/AllClass.R (symmetricMatrix): add validity method (available
384            in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
385    
386            * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
387    
388            * tests/indexing.Rout.save:
389            * tests/indexing.R: additions, mainly for 'lsparse'
390    
391            * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
392            case.
393    
394            * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
395    
396    2006-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
397    
398            * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
399                    as 'N' (1-letter - Ok?)
400    
401            * tests/group-methods.R: add test for logical + NAs
402    
403            * R/dMatrix.R ("Compare"): fix to work with NA's
404    
405            * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
406    
407            * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
408                    which is implemented.
409    
410    2006-09-15  Martin Maechler  <maechler@stat.math.ethz.ch>
411    
412            * src/chm_common.c: coerce logical <-> double instead of
413            typecasting;  needed for "l" matrix handling in cholmod.
414    
415            * tests/other-pkgs.R (graph): small extension in "graph" checks.
416    
417            * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
418            (Tsp2grNEL): other fixes needed
419    
420  2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
421    
422          * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"          * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
# Line 7  Line 426 
426          * tests/: adaptions          * tests/: adaptions
427          * src/chm_common.c (chm_dense_to_SEXP): and others:          * src/chm_common.c (chm_dense_to_SEXP): and others:
428                  new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL                  new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
429          * src/Csparse.c, etc: dito          * src/Csparse.c, etc: ditto
430    
431  2006-09-11  Douglas Bates  <bates@R-project.org>  2006-09-11  Douglas Bates  <bates@R-project.org>
432    
# Line 26  Line 445 
445          * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()          * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
446    
447          * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"          * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
448          * man/tcrossprod.Rd: dito          * man/tcrossprod.Rd: ditto
449    
450  2006-09-08  Douglas Bates  <bates@stat.wisc.edu>  2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
451    
# Line 69  Line 488 
488    
489          * R/sparseMatrix.R (Arith): moved Arith group method one-level up          * R/sparseMatrix.R (Arith): moved Arith group method one-level up
490          from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"          from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
491          * R/dsparseMatrix.R: dito          * R/dsparseMatrix.R: ditto
492          * R/Csparse.R: dito          * R/Csparse.R: ditto
493    
494  2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
495    
# Line 86  Line 505 
505    
506          * 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
507          * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.          * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
508          (.is.diagonal): dito          (.is.diagonal): ditto
509    
510          * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's          * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
511    

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