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revision 1455, Mon Aug 28 15:35:44 2006 UTC revision 1691, Sun Dec 10 13:54:15 2006 UTC
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1    2006-12-10  Douglas Bates  <bates@stat.wisc.edu>
2    
3            * src/CHMfactor.c (CHMfactor_to_sparse): change LDL factorization
4            to LL before converting to a sparse matrix. (The LDL form can be
5            converted to a sparse matrix but it is implicitly a unit
6            triangular matrix and a diagonal matrix overwritten on the diagonal.)
7    
8    2006-12-09  Douglas Bates  <bates@stat.wisc.edu>
9    
10            * src/chm_common.c (chm_factor_to_SEXP): allocate and fill the Dim slot.
11    
12    2006-12-08  Douglas Bates  <bates@stat.wisc.edu>
13    
14            * DESCRIPTION (Version): updated -> release 0.9975-7
15            * src/{init.c,chm_common.c}, inst/include/*: export cholmod_analyze_p
16    
17    2006-11-30  Martin Maechler  <maechler@stat.math.ethz.ch>
18    
19            * R/diagMatrix.R (%*%): write a direct [diag o Csparse] method
20    
21    2006-11-29  Douglas Bates  <bates@stat.wisc.edu>
22    
23            * src/dgeMatrix.c (dgeMatrix_solve): Check error code from dgetri.
24            * tests/dg_Matrix.R: Add Barry Rowlingson's test of a matrix that
25            is exactly singular.
26    
27    2006-11-07  Martin Maechler  <maechler@stat.math.ethz.ch>
28    
29            * DESCRIPTION (Date): updated -> release 0.9975-6
30    
31    2006-11-06  Martin Maechler  <maechler@stat.math.ethz.ch>
32    
33            * R/Csparse.R (replCmat): symmetric indexing of symmetric matrix
34            now returns symmetric.
35    
36            * R/zzz.R ("diag<-"): replace "diag<-" in base for R <= 2.4.x
37    
38            * R/Matrix.R (.M.sub.i.2col):  new, for  M[ cbind(i,j) ] indexing.
39            * R/Matrix.R (.M.repl.i.2col): new, for  M[ cbind(i,j) ] <- value
40    
41            * R/Auxiliaries.R (.type.kind): added
42    
43    2006-11-04  Martin Maechler  <maechler@stat.math.ethz.ch>
44    
45            * src/cs.[ch]: updated to CSparse Version 2.0.3 by simply
46            running src/CSparse_install.sh
47    
48            * R/denseMatrix.R: "[": keep symmetric on symmetric indexing.
49    
50    2006-11-03  Martin Maechler  <maechler@stat.math.ethz.ch>
51    
52            * src/dsCMatrix.c (dsCMatrix_Csparse_solve): new
53            * R/dsCMatrix.R (solve): "fully-sparse" using the above.
54    
55            * R/AllClass.R: "pMatrix" now also inherits from "generalMatrix"
56    
57            * tests/Class+Meth.R (tstMatrixClass): now assure
58            the (important in method programming) property :
59    
60                    ###>>  Every "Matrix" is either
61                    ###>>  "general*", "symmetric*", "triangular*" or "diagonal*"
62    
63                    (where "*" stands for "Matrix")
64    
65            * R/Auxiliaries.R (diagU2N): now .Call()s Csparse_diagU2N for <Csparse>
66    
67            * R/dMatrix.R (Compare(<dMatrix>,<dMatrix>): update and
68            * tests/validObj.R: checks for "comparison"
69    
70            * R/sparseMatrix.R ([): improved indexing for sparse;
71                    trying to keep <symmetric>[ n, n] symmmetric
72    
73            * tests/indexing.R: indexing for logical sparse now ok
74    
75    
76    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
77    
78            * src/Tsparse.c: use xTsparse_validate() , and hence remove
79    
80            * src/{ltC,lsC,lgT}Matrix.[ch]: removed
81    
82    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
83    
84            * R/AllClass.R (Matrix-class): check length of dimnames in validity.
85    
86            * tests/simple.R: validObject() checking the above.
87    
88            * src/dgCMatrix.c (xCMatrix_validate): new, small and simple,
89            replacing both dgCMatrix_validate and lgCM*.
90    
91            * src/Csparse.c (Csparse_dense_prod, etc): do not lose dimnames;
92            fix dimnames setting in other places.
93            * src/chm_common.c (chm_dense_to_SEXP): now can pass dimnames
94    
95    2006-11-01  Martin Maechler  <maechler@stat.math.ethz.ch>
96    
97            * R/Csparse.R,src/Csparse.c, etc: tcrossprod(<CsparseM>,<CsparseM>)
98    
99            * R/sparseMatrix.R (isSymmetric): drop 'factors' slot for
100            symmetry test, via
101            * R/Auxiliaries.R (.as.dgC.0.factors):
102    
103    2006-11-01  Douglas Bates  <bates@r-project.org>
104    
105            * R/Csparse.R,src/Csparse.c,tests/matprod.R,
106            man/CsparseMatrix-class.Rd: crossprod(<CsparseMatrix>,
107            <CsparseMatrix>) added
108    
109    2006-10-30  Martin Maechler  <maechler@stat.math.ethz.ch>
110    
111            * tests/matprod.R: add a variation of Harri's example
112    
113            * R/dsparseMatrix.R: fix crossprod(<dsparse>, <dge>) to *not*
114            recursive infinitely.
115    
116            * R/dgCMatrix.R: + solve(<sparse>, <sparse>)
117    
118            * tests/indexing.R: add test for the "<" bug fixed 10-27 in R/dMatrix.R
119    
120    2006-10-28  Martin Maechler  <maechler@stat.math.ethz.ch>
121    
122            * tests/Class+Meth.R (tstMatrixClass): more: use non-trivial
123            matrix if possible; test m+m == 2*m; now test dgRMatrix.
124            * R/dgRMatrix.R (.to.dgR): a few more coercions, in order to
125            satisfy the above test.
126    
127    2006-10-27  Martin Maechler  <maechler@stat.math.ethz.ch>
128    
129            * R/Matrix.R (Ops):  <Matrix> o <matrix>  method added
130    
131            * R/dgCMatrix.R: solve(a, b="missing") based on
132            * src/dgCMatrix.c (dgCMatrix_matrix_solve): extend to work with
133            RHS = NULL.
134    
135            * R/diagMatrix.R (diagdiagprod): extend %*% etc to ldiMatrix;
136            add more (needed) [t]crossprod() methods.
137    
138            * man/ddiMatrix-class.Rd: more info, notably on 'diag'
139    
140            * R/Auxiliaries.R (as_CspClass): cleanup
141            (drop0): internal utility for "Csparse_drop(*, 0)"
142            (.bail.out.2): encourage active feedback
143    
144    2006-10-26  Martin Maechler  <maechler@stat.math.ethz.ch>
145    
146            * R/dMatrix.R(Compare): new(), then slots [no validity check]
147    
148            * src/Csparse.c (Csparse_validate): fixed (and more efficient in
149            non-valid or 'sorted' case).
150    
151            * R/dsparseMatrix.R: add "chol" method.
152            * R/ddenseMatrix.R: ditto
153    
154            * R/diagMatrix.R (Ops): group methods for  <diagonal> o <sparse>
155            * NAMESPACE (Ops)
156            * R/diagMatrix.R (diag2T): simple utility used "higher level"
157            coercion; deprecating direct lower level coercions.
158    
159            * R/*.R (seq): use seq_len() and seq_along() where possible.
160    
161    
162    2006-10-23  Martin Maechler  <maechler@stat.math.ethz.ch>
163    
164            * DESCRIPTION (Version): 0.9975-5 ready for release
165    
166    2006-10-20  Douglas Bates  <bates@stat.wisc.edu>
167    
168            * src/init.c (R_init_Matrix): export more cholmod CCallable functions.
169    
170    2006-10-20  Martin Maechler  <maechler@stat.math.ethz.ch>
171    
172            * R/AllClass.R (corMatrix): add 'validity' check;
173                    comment out unused "LDL" class definition
174            * NAMESPACE: mention, but do not export "LDL" class
175            * R/corMatrix.R: new (simple), needed for R-devel with
176            * tests/Class+Meth.R (tstMatrixClass): 1 exception for corMatrix
177              coerce and t() exceptions for all 5 'Mat.MatFact' classes.
178    
179    2006-10-19  Douglas Bates  <bates@stat.wisc.edu>
180    
181            * src/chm_common.h: Add R_cholmod_start to initialize cholmod to
182            use Rprintf and R's error handling.
183    
184    2006-10-17  Martin Maechler  <maechler@stat.math.ethz.ch>
185    
186            * R/diagMatrix.R (%*%): rep(*, each = .) in Matrix %*% diagonal.
187            * tests/matprod.R: add tests for the bug fixed.
188    
189    2006-10-11  Douglas Bates  <bates@stat.wisc.edu>
190    
191            * src/HBMM.[ch]: remove HarwellBoeing format for writing.
192            * src/SOURCES_C.mkf (SOURCES_C): no longer compile iohb.c
193    
194    2006-10-06  Douglas Bates  <bates@stat.wisc.edu>
195    
196            * R/d[gs]CMatrix.R: deprecate the writeHB function.  Use writeMM instead.
197    
198    2006-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
199    
200            * DESCRIPTION (Version): 0.9975-3
201    
202            * R/diagMatrix.R (bdiag): new function constructing block diagonal
203            (sparse) matrices.
204            * man/bdiag.Rd: docu + examples
205    
206            * R/Csparse.R (replCmat): calling new Csparse_drop() now.
207    
208            * src/Csparse.c (Csparse_general_to_symmetric, Csparse_drop): new functions
209            * R/lsCMatrix.R: three more coercions to lsC (thanks to the above)
210    
211            * R/diagMatrix.R (Diagonal): '[<-' method for diag.matrices such
212            that result is sparse or diagonal (and not dense).
213    
214            * man/Subassign-methods.Rd: fix examples
215    
216            * R/Matrix.R (Matrix):  Matrix(0, *) or Matrix(*, sparse=TRUE)
217            should always return a sparse (and not sometimes a diagonal) matrix.
218    
219    2006-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
220    
221            * R/Matrix.R ([<-): also for value "Matrix" or "matrix"
222    
223    2006-10-04  Douglas Bates  <bates@stat.wisc.edu>
224    
225            * DESCRIPTION (Version): 0.9975-2
226    
227            * inst/include/Matrix_stubs.c (M_cholmod_sparse_to_triplet): export more symbols
228    
229    2006-10-02  Douglas Bates  <bates@R-project.org>
230    
231            * tests/dg_Matrix.R: Simplify test taking into account new code.
232    
233    2006-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
234    
235            * R/Csparse.R (replCmat): improve for missing i / j in non-simple cases
236    
237            * R/lsTMatrix.R: new files w/ missing methods
238            * R/nsTMatrix.R:  "  'for completeness'
239    
240            * tests/Class+Meth.R: a bit less 'not.ok.classes'
241    
242            * R/Tsparse.R (t): generalized "t" method from "dgT*" to "Tsparse*"
243    
244    
245    2006-09-28  Douglas Bates  <bates@R-project.org>
246    
247            * src/dppMatrix.h: Ensure definition of dspMatrix_validate is
248            included.
249    
250            * src/init.c, inst/include/{Matrix.h,Matrix_stubs.h,cholmod.h}:
251            Export C-callable functions used in Zt_create in lme4.
252    
253    2006-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
254    
255            * DESCRIPTION (Version): 0.9975-1
256    
257            * tests/simple.R: less checks fail; using NA, found that our
258                    kronecker() is not base-compatible with NA's.
259    
260            * R/dMatrix.R: "Compare" method now implemented for all cases
261    
262            * R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility
263    
264            * man/dtpMatrix-class.Rd: mention length of 'x' slot
265    
266            * src/dtpMatrix.c (dtpMatrix_validate): fix check
267            * src/dspMatrix.c (dspMatrix_validate): ditto
268    
269            * R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
270              including coercion to [nl]tTMatrix.
271    
272            * R/diagMatrix.R (show): print a header line as for other classes.
273    
274    2006-09-27  Martin Maechler  <maechler@stat.math.ethz.ch>
275    
276            * src/Makefile.win (SUBDIRS): fix typo
277    
278    2006-09-19  Martin Maechler  <maechler@stat.math.ethz.ch>
279    
280            * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
281    
282    2006-09-18  Douglas Bates  <bates@stat.wisc.edu>
283    
284            * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
285            symmetric and y missing in R code using %*% (cholmod_aat doesn't
286            accept a symmetric matrix).
287            * tests/group-methods.R: Uncomment test of crossprod applied to
288            lsCMatrix objects.
289    
290    2006-09-18  Martin Maechler  <maechler@stat.math.ethz.ch>
291    
292            * R/AllClass.R (symmetricMatrix): add validity method (available
293            in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
294    
295            * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
296    
297            * tests/indexing.Rout.save:
298            * tests/indexing.R: additions, mainly for 'lsparse'
299    
300            * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
301            case.
302    
303            * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
304    
305    2006-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
306    
307            * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
308                    as 'N' (1-letter - Ok?)
309    
310            * tests/group-methods.R: add test for logical + NAs
311    
312            * R/dMatrix.R ("Compare"): fix to work with NA's
313    
314            * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
315    
316            * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
317                    which is implemented.
318    
319    2006-09-15  Martin Maechler  <maechler@stat.math.ethz.ch>
320    
321            * src/chm_common.c: coerce logical <-> double instead of
322            typecasting;  needed for "l" matrix handling in cholmod.
323    
324            * tests/other-pkgs.R (graph): small extension in "graph" checks.
325    
326            * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
327            (Tsp2grNEL): other fixes needed
328    
329    2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
330    
331            * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
332                    Matrices, since "lMatrix", also "lsparseM" can have NA
333            * R/ndenseMatrix.R, etc: new source files
334            * man/nsparseMatrix-classes.Rd, etc: new help files
335            * tests/: adaptions
336            * src/chm_common.c (chm_dense_to_SEXP): and others:
337                    new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
338            * src/Csparse.c, etc: ditto
339    
340    2006-09-11  Douglas Bates  <bates@R-project.org>
341    
342            * src/Mutils.[ch],init.c inst/include/*.h: Move the
343            alloc_d**Matrix functions to the lme4 package.
344    
345    2006-09-09  Douglas Bates  <bates@R-project.org>
346    
347            * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
348            fixed
349    
350    2006-09-09  Martin Maechler  <maechler@stat.math.ethz.ch>
351    
352            * R/lMatrix.R: new
353    
354            * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
355    
356            * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
357            * man/tcrossprod.Rd: ditto
358    
359    2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
360    
361            * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
362            for exported functions
363            * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
364            Remove partitioning algorithms for sparse matrix reordering.  The
365            copyright on the Metis code was problematic and the methods were
366            rarely used.
367            * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
368            operations are now done entirely in CHOLMOD code.
369    
370    2006-09-06  Douglas Bates  <bates@R-project.org>
371    
372            * src/Mutils.h: Remove functions that are no longer used.
373    
374    2006-09-04  Douglas Bates  <bates@R-project.org>
375    
376            * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
377            * src/DEPS.mkf: update
378    
379    2006-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>
380    
381            * created branches/Matrix-for-R-2.3.x;  on trunk: do
382            * DESCRIPTION (Version): 0.9975-0
383            (Depends): R (>= 2.4.0)
384    
385    2006-09-01  Douglas Bates  <bates@R-project.org>
386    
387            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
388    
389    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
390    
391            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
392            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
393    
394            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
395    
396    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
397    
398            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
399            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
400            * R/dsparseMatrix.R: ditto
401            * R/Csparse.R: ditto
402    
403    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
404    
405            * R/dMatrix.R (Compare): improve availability of "<", etc
406            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
407    
408    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
409    
410            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
411            of a 0-index which was used as 1-index (..hmm)
412    
413            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
414    
415            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
416            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
417            (.is.diagonal): ditto
418    
419            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
420    
421            * R/Matrix.R (Matrix): also work for NA data
422    
423  2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
424    
425          * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting          * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting

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