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revision 1455, Mon Aug 28 15:35:44 2006 UTC revision 1710, Tue Dec 26 15:57:06 2006 UTC
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1    2006-12-26  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * DESCRIPTION (Date, Version): 0.9975-8, ready for release
4    
5            * R/Tsparse.R (replTmat): fix subassignment of triangular
6            * R/Csparse.R (replCmat): ditto
7            * tests/indexing.R: more tests, incl the above fix
8    
9    2006-12-23  Martin Maechler  <maechler@stat.math.ethz.ch>
10    
11            * R/Auxiliaries.R (drop0): extend for non CSparse
12            * R/Auxiliaries.R (diagU2N): should work for all sparseMatrix
13    
14            * src/Csparse.c (Csparse_to_Tsparse, Csparse_general_to_symmetric):
15                    use uplo correctly (!); other places: use uplo_P() macro
16    
17            * R/Csparse.R (replCmat): call diagU2N() when needed
18            * R/Tsparse.R (replTmat): ditto
19    
20            * src/dtCMatrix.c (tCMatrix_validate): new
21            * src/dtTMatrix.c (tTMatrix_validate): new, used in
22            * R/AllClass.R: for validity of dtC, dsC, and dtT, dsT.
23    
24            * R/diagMatrix.R (replDiag): to use in [<-
25    
26    2006-12-22  Martin Maechler  <maechler@stat.math.ethz.ch>
27    
28            * R/Auxiliaries.R (as_Csparse2, as_geSimpl): new functions;
29                    also more general diagU2N().
30    
31    2006-12-21  Martin Maechler  <maechler@stat.math.ethz.ch>
32    
33            * R/bind2.R: new file for all cbind2(), rbind() methods moved here
34            from R/<foo>Matrix.R files. Better diagonal & improved sparse methods.
35    
36    2006-12-20  Martin Maechler  <maechler@stat.math.ethz.ch>
37    
38            * tests/bind.R: a few more cases
39            * R/Auxiliaries.R (.M.kind): also work for atomic vectors
40    
41            * R/denseMatrix.R (cbind2/rbind2): moved here (and generalized) from
42            * R/ddenseMatrix.R (cbind2/rbind2)
43            * R/Tsparse.R (replTmat): final(?!) fix for "[<-" ..
44            * tests/indexing.R
45            * tests/indexing.Rout.save: updated
46    
47    2006-12-18  Martin Maechler  <maechler@stat.math.ethz.ch>
48    
49            * R/Tsparse.R (replTmat): fixed a remaining "[<-" bug in
50            * tests/indexing.R
51    
52    2006-12-15  Martin Maechler  <maechler@stat.math.ethz.ch>
53    
54            * R/sparseMatrix.R (prSpMatrix): "." alignment much improved:
55            align with proper position of "0", i.e., right for integers.
56            argument 'align' by default is "fancy".
57    
58    2006-12-14  Martin Maechler  <maechler@stat.math.ethz.ch>
59    
60            * R/sparseMatrix.R: delegate "Compare" to "Csparse.."
61            * R/Csparse.R: and fix "Compare" for more cases.
62            * tests/Class+Meth.R: test some of these (m == m, m != m)
63    
64    2006-12-13  Martin Maechler  <maechler@stat.math.ethz.ch>
65    
66            * R/lsparseMatrix.R: all() and any() methods
67            * R/ldenseMatrix.R:      ditto
68            * NAMESPACE, R/Matrix.R: ditto
69    
70            * man/all-methods.Rd: document them minimally
71    
72            * tests/simple.R: add a few examples for these
73    
74    2006-12-11  Martin Maechler  <maechler@stat.math.ethz.ch>
75    
76            * R/Tsparse.R ([): fix long standing typo in symmetric case
77            * man/dsCMatrix-class.Rd: add example exhibiting the above case
78    
79    2006-12-10  Douglas Bates  <bates@stat.wisc.edu>
80    
81            * src/CHMfactor.c (CHMfactor_to_sparse): change LDL factorization
82            to LL before converting to a sparse matrix. (The LDL form can be
83            converted to a sparse matrix but it is implicitly a unit
84            triangular matrix and a diagonal matrix overwritten on the diagonal.)
85    
86    2006-12-09  Douglas Bates  <bates@stat.wisc.edu>
87    
88            * src/chm_common.c (chm_factor_to_SEXP): allocate and fill the Dim slot.
89    
90    2006-12-08  Douglas Bates  <bates@stat.wisc.edu>
91    
92            * DESCRIPTION (Version): updated -> release 0.9975-7
93            * src/{init.c,chm_common.c}, inst/include/*: export cholmod_analyze_p
94    
95    2006-11-30  Martin Maechler  <maechler@stat.math.ethz.ch>
96    
97            * R/diagMatrix.R (%*%): write a direct [diag o Csparse] method
98    
99    2006-11-29  Douglas Bates  <bates@stat.wisc.edu>
100    
101            * src/dgeMatrix.c (dgeMatrix_solve): Check error code from dgetri.
102            * tests/dg_Matrix.R: Add Barry Rowlingson's test of a matrix that
103            is exactly singular.
104    
105    2006-11-07  Martin Maechler  <maechler@stat.math.ethz.ch>
106    
107            * DESCRIPTION (Date): updated -> release 0.9975-6
108    
109    2006-11-06  Martin Maechler  <maechler@stat.math.ethz.ch>
110    
111            * R/Csparse.R (replCmat): symmetric indexing of symmetric matrix
112            now returns symmetric.
113    
114            * R/zzz.R ("diag<-"): replace "diag<-" in base for R <= 2.4.x
115    
116            * R/Matrix.R (.M.sub.i.2col):  new, for  M[ cbind(i,j) ] indexing.
117            * R/Matrix.R (.M.repl.i.2col): new, for  M[ cbind(i,j) ] <- value
118    
119            * R/Auxiliaries.R (.type.kind): added
120    
121    2006-11-04  Martin Maechler  <maechler@stat.math.ethz.ch>
122    
123            * src/cs.[ch]: updated to CSparse Version 2.0.3 by simply
124            running src/CSparse_install.sh
125    
126            * R/denseMatrix.R: "[": keep symmetric on symmetric indexing.
127    
128    2006-11-03  Martin Maechler  <maechler@stat.math.ethz.ch>
129    
130            * src/dsCMatrix.c (dsCMatrix_Csparse_solve): new
131            * R/dsCMatrix.R (solve): "fully-sparse" using the above.
132    
133            * R/AllClass.R: "pMatrix" now also inherits from "generalMatrix"
134    
135            * tests/Class+Meth.R (tstMatrixClass): now assure
136            the (important in method programming) property :
137    
138                    ###>>  Every "Matrix" is either
139                    ###>>  "general*", "symmetric*", "triangular*" or "diagonal*"
140    
141                    (where "*" stands for "Matrix")
142    
143            * R/Auxiliaries.R (diagU2N): now .Call()s Csparse_diagU2N for <Csparse>
144    
145            * R/dMatrix.R (Compare(<dMatrix>,<dMatrix>): update and
146            * tests/validObj.R: checks for "comparison"
147    
148            * R/sparseMatrix.R ([): improved indexing for sparse;
149                    trying to keep <symmetric>[ n, n] symmmetric
150    
151            * tests/indexing.R: indexing for logical sparse now ok
152    
153    
154    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
155    
156            * src/Tsparse.c: use xTsparse_validate() , and hence remove
157    
158            * src/{ltC,lsC,lgT}Matrix.[ch]: removed
159    
160    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
161    
162            * R/AllClass.R (Matrix-class): check length of dimnames in validity.
163    
164            * tests/simple.R: validObject() checking the above.
165    
166            * src/dgCMatrix.c (xCMatrix_validate): new, small and simple,
167            replacing both dgCMatrix_validate and lgCM*.
168    
169            * src/Csparse.c (Csparse_dense_prod, etc): do not lose dimnames;
170            fix dimnames setting in other places.
171            * src/chm_common.c (chm_dense_to_SEXP): now can pass dimnames
172    
173    2006-11-01  Martin Maechler  <maechler@stat.math.ethz.ch>
174    
175            * R/Csparse.R,src/Csparse.c, etc: tcrossprod(<CsparseM>,<CsparseM>)
176    
177            * R/sparseMatrix.R (isSymmetric): drop 'factors' slot for
178            symmetry test, via
179            * R/Auxiliaries.R (.as.dgC.0.factors):
180    
181    2006-11-01  Douglas Bates  <bates@r-project.org>
182    
183            * R/Csparse.R,src/Csparse.c,tests/matprod.R,
184            man/CsparseMatrix-class.Rd: crossprod(<CsparseMatrix>,
185            <CsparseMatrix>) added
186    
187    2006-10-30  Martin Maechler  <maechler@stat.math.ethz.ch>
188    
189            * tests/matprod.R: add a variation of Harri's example
190    
191            * R/dsparseMatrix.R: fix crossprod(<dsparse>, <dge>) to *not*
192            recursive infinitely.
193    
194            * R/dgCMatrix.R: + solve(<sparse>, <sparse>)
195    
196            * tests/indexing.R: add test for the "<" bug fixed 10-27 in R/dMatrix.R
197    
198    2006-10-28  Martin Maechler  <maechler@stat.math.ethz.ch>
199    
200            * tests/Class+Meth.R (tstMatrixClass): more: use non-trivial
201            matrix if possible; test m+m == 2*m; now test dgRMatrix.
202            * R/dgRMatrix.R (.to.dgR): a few more coercions, in order to
203            satisfy the above test.
204    
205    2006-10-27  Martin Maechler  <maechler@stat.math.ethz.ch>
206    
207            * R/Matrix.R (Ops):  <Matrix> o <matrix>  method added
208    
209            * R/dgCMatrix.R: solve(a, b="missing") based on
210            * src/dgCMatrix.c (dgCMatrix_matrix_solve): extend to work with
211            RHS = NULL.
212    
213            * R/diagMatrix.R (diagdiagprod): extend %*% etc to ldiMatrix;
214            add more (needed) [t]crossprod() methods.
215    
216            * man/ddiMatrix-class.Rd: more info, notably on 'diag'
217    
218            * R/Auxiliaries.R (as_CspClass): cleanup
219            (drop0): internal utility for "Csparse_drop(*, 0)"
220            (.bail.out.2): encourage active feedback
221    
222    2006-10-26  Martin Maechler  <maechler@stat.math.ethz.ch>
223    
224            * R/dMatrix.R(Compare): new(), then slots [no validity check]
225    
226            * src/Csparse.c (Csparse_validate): fixed (and more efficient in
227            non-valid or 'sorted' case).
228    
229            * R/dsparseMatrix.R: add "chol" method.
230            * R/ddenseMatrix.R: ditto
231    
232            * R/diagMatrix.R (Ops): group methods for  <diagonal> o <sparse>
233            * NAMESPACE (Ops)
234            * R/diagMatrix.R (diag2T): simple utility used "higher level"
235            coercion; deprecating direct lower level coercions.
236    
237            * R/*.R (seq): use seq_len() and seq_along() where possible.
238    
239    
240    2006-10-23  Martin Maechler  <maechler@stat.math.ethz.ch>
241    
242            * DESCRIPTION (Version): 0.9975-5 ready for release
243    
244    2006-10-20  Douglas Bates  <bates@stat.wisc.edu>
245    
246            * src/init.c (R_init_Matrix): export more cholmod CCallable functions.
247    
248    2006-10-20  Martin Maechler  <maechler@stat.math.ethz.ch>
249    
250            * R/AllClass.R (corMatrix): add 'validity' check;
251                    comment out unused "LDL" class definition
252            * NAMESPACE: mention, but do not export "LDL" class
253            * R/corMatrix.R: new (simple), needed for R-devel with
254            * tests/Class+Meth.R (tstMatrixClass): 1 exception for corMatrix
255              coerce and t() exceptions for all 5 'Mat.MatFact' classes.
256    
257    2006-10-19  Douglas Bates  <bates@stat.wisc.edu>
258    
259            * src/chm_common.h: Add R_cholmod_start to initialize cholmod to
260            use Rprintf and R's error handling.
261    
262    2006-10-17  Martin Maechler  <maechler@stat.math.ethz.ch>
263    
264            * R/diagMatrix.R (%*%): rep(*, each = .) in Matrix %*% diagonal.
265            * tests/matprod.R: add tests for the bug fixed.
266    
267    2006-10-11  Douglas Bates  <bates@stat.wisc.edu>
268    
269            * src/HBMM.[ch]: remove HarwellBoeing format for writing.
270            * src/SOURCES_C.mkf (SOURCES_C): no longer compile iohb.c
271    
272    2006-10-06  Douglas Bates  <bates@stat.wisc.edu>
273    
274            * R/d[gs]CMatrix.R: deprecate the writeHB function.  Use writeMM instead.
275    
276    2006-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
277    
278            * DESCRIPTION (Version): 0.9975-3
279    
280            * R/diagMatrix.R (bdiag): new function constructing block diagonal
281            (sparse) matrices.
282            * man/bdiag.Rd: docu + examples
283    
284            * R/Csparse.R (replCmat): calling new Csparse_drop() now.
285    
286            * src/Csparse.c (Csparse_general_to_symmetric, Csparse_drop): new functions
287            * R/lsCMatrix.R: three more coercions to lsC (thanks to the above)
288    
289            * R/diagMatrix.R (Diagonal): '[<-' method for diag.matrices such
290            that result is sparse or diagonal (and not dense).
291    
292            * man/Subassign-methods.Rd: fix examples
293    
294            * R/Matrix.R (Matrix):  Matrix(0, *) or Matrix(*, sparse=TRUE)
295            should always return a sparse (and not sometimes a diagonal) matrix.
296    
297    2006-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
298    
299            * R/Matrix.R ([<-): also for value "Matrix" or "matrix"
300    
301    2006-10-04  Douglas Bates  <bates@stat.wisc.edu>
302    
303            * DESCRIPTION (Version): 0.9975-2
304    
305            * inst/include/Matrix_stubs.c (M_cholmod_sparse_to_triplet): export more symbols
306    
307    2006-10-02  Douglas Bates  <bates@R-project.org>
308    
309            * tests/dg_Matrix.R: Simplify test taking into account new code.
310    
311    2006-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
312    
313            * R/Csparse.R (replCmat): improve for missing i / j in non-simple cases
314    
315            * R/lsTMatrix.R: new files w/ missing methods
316            * R/nsTMatrix.R:  "  'for completeness'
317    
318            * tests/Class+Meth.R: a bit less 'not.ok.classes'
319    
320            * R/Tsparse.R (t): generalized "t" method from "dgT*" to "Tsparse*"
321    
322    
323    2006-09-28  Douglas Bates  <bates@R-project.org>
324    
325            * src/dppMatrix.h: Ensure definition of dspMatrix_validate is
326            included.
327    
328            * src/init.c, inst/include/{Matrix.h,Matrix_stubs.h,cholmod.h}:
329            Export C-callable functions used in Zt_create in lme4.
330    
331    2006-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
332    
333            * DESCRIPTION (Version): 0.9975-1
334    
335            * tests/simple.R: less checks fail; using NA, found that our
336                    kronecker() is not base-compatible with NA's.
337    
338            * R/dMatrix.R: "Compare" method now implemented for all cases
339    
340            * R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility
341    
342            * man/dtpMatrix-class.Rd: mention length of 'x' slot
343    
344            * src/dtpMatrix.c (dtpMatrix_validate): fix check
345            * src/dspMatrix.c (dspMatrix_validate): ditto
346    
347            * R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
348              including coercion to [nl]tTMatrix.
349    
350            * R/diagMatrix.R (show): print a header line as for other classes.
351    
352    2006-09-27  Martin Maechler  <maechler@stat.math.ethz.ch>
353    
354            * src/Makefile.win (SUBDIRS): fix typo
355    
356    2006-09-19  Martin Maechler  <maechler@stat.math.ethz.ch>
357    
358            * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
359    
360    2006-09-18  Douglas Bates  <bates@stat.wisc.edu>
361    
362            * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
363            symmetric and y missing in R code using %*% (cholmod_aat doesn't
364            accept a symmetric matrix).
365            * tests/group-methods.R: Uncomment test of crossprod applied to
366            lsCMatrix objects.
367    
368    2006-09-18  Martin Maechler  <maechler@stat.math.ethz.ch>
369    
370            * R/AllClass.R (symmetricMatrix): add validity method (available
371            in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
372    
373            * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
374    
375            * tests/indexing.Rout.save:
376            * tests/indexing.R: additions, mainly for 'lsparse'
377    
378            * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
379            case.
380    
381            * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
382    
383    2006-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
384    
385            * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
386                    as 'N' (1-letter - Ok?)
387    
388            * tests/group-methods.R: add test for logical + NAs
389    
390            * R/dMatrix.R ("Compare"): fix to work with NA's
391    
392            * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
393    
394            * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
395                    which is implemented.
396    
397    2006-09-15  Martin Maechler  <maechler@stat.math.ethz.ch>
398    
399            * src/chm_common.c: coerce logical <-> double instead of
400            typecasting;  needed for "l" matrix handling in cholmod.
401    
402            * tests/other-pkgs.R (graph): small extension in "graph" checks.
403    
404            * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
405            (Tsp2grNEL): other fixes needed
406    
407    2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
408    
409            * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
410                    Matrices, since "lMatrix", also "lsparseM" can have NA
411            * R/ndenseMatrix.R, etc: new source files
412            * man/nsparseMatrix-classes.Rd, etc: new help files
413            * tests/: adaptions
414            * src/chm_common.c (chm_dense_to_SEXP): and others:
415                    new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
416            * src/Csparse.c, etc: ditto
417    
418    2006-09-11  Douglas Bates  <bates@R-project.org>
419    
420            * src/Mutils.[ch],init.c inst/include/*.h: Move the
421            alloc_d**Matrix functions to the lme4 package.
422    
423    2006-09-09  Douglas Bates  <bates@R-project.org>
424    
425            * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
426            fixed
427    
428    2006-09-09  Martin Maechler  <maechler@stat.math.ethz.ch>
429    
430            * R/lMatrix.R: new
431    
432            * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
433    
434            * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
435            * man/tcrossprod.Rd: ditto
436    
437    2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
438    
439            * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
440            for exported functions
441            * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
442            Remove partitioning algorithms for sparse matrix reordering.  The
443            copyright on the Metis code was problematic and the methods were
444            rarely used.
445            * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
446            operations are now done entirely in CHOLMOD code.
447    
448    2006-09-06  Douglas Bates  <bates@R-project.org>
449    
450            * src/Mutils.h: Remove functions that are no longer used.
451    
452    2006-09-04  Douglas Bates  <bates@R-project.org>
453    
454            * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
455            * src/DEPS.mkf: update
456    
457    2006-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>
458    
459            * created branches/Matrix-for-R-2.3.x;  on trunk: do
460            * DESCRIPTION (Version): 0.9975-0
461            (Depends): R (>= 2.4.0)
462    
463    2006-09-01  Douglas Bates  <bates@R-project.org>
464    
465            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
466    
467    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
468    
469            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
470            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
471    
472            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
473    
474    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
475    
476            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
477            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
478            * R/dsparseMatrix.R: ditto
479            * R/Csparse.R: ditto
480    
481    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
482    
483            * R/dMatrix.R (Compare): improve availability of "<", etc
484            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
485    
486    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
487    
488            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
489            of a 0-index which was used as 1-index (..hmm)
490    
491            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
492    
493            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
494            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
495            (.is.diagonal): ditto
496    
497            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
498    
499            * R/Matrix.R (Matrix): also work for NA data
500    
501  2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
502    
503          * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting          * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting

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