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revision 1445, Fri Aug 25 14:54:54 2006 UTC revision 1624, Wed Oct 11 15:00:11 2006 UTC
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1    2006-10-11  Douglas Bates  <bates@stat.wisc.edu>
2    
3            * src/HBMM.[ch]: remove HarwellBoeing format for writing.
4            * src/SOURCES_C.mkf (SOURCES_C): no longer compile iohb.c
5    
6    2006-10-06  Douglas Bates  <bates@stat.wisc.edu>
7    
8            * R/dgCMatrix.R: deprecate the writeHB function.  Use writeMM instead.
9    
10    2006-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
11    
12            * DESCRIPTION (Version): 0.9975-3
13    
14            * R/diagMatrix.R (bdiag): new function constructing block diagonal
15            (sparse) matrices.
16            * man/bdiag.Rd: docu + examples
17    
18            * R/Csparse.R (replCmat): calling new Csparse_drop() now.
19    
20            * src/Csparse.c (Csparse_general_to_symmetric, Csparse_drop): new functions
21            * R/lsCMatrix.R: three more coercions to lsC (thanks to the above)
22    
23            * R/diagMatrix.R (Diagonal): '[<-' method for diag.matrices such
24            that result is sparse or diagonal (and not dense).
25    
26            * man/Subassign-methods.Rd: fix examples
27    
28            * R/Matrix.R (Matrix):  Matrix(0, *) or Matrix(*, sparse=TRUE)
29            should always return a sparse (and not sometimes a diagonal) matrix.
30    
31    2006-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
32    
33            * R/Matrix.R ([<-): also for value "Matrix" or "matrix"
34    
35    2006-10-04  Douglas Bates  <bates@stat.wisc.edu>
36    
37            * DESCRIPTION (Version): 0.9975-2
38    
39            * inst/include/Matrix_stubs.c (M_cholmod_sparse_to_triplet): export more symbols
40    
41    2006-10-02  Douglas Bates  <bates@R-project.org>
42    
43            * tests/dg_Matrix.R: Simplify test taking into account new code.
44    
45    2006-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
46    
47            * R/Csparse.R (replCmat): improve for missing i / j in non-simple cases
48    
49            * R/lsTMatrix.R: new files w/ missing methods
50            * R/nsTMatrix.R:  "  'for completeness'
51    
52            * tests/Class+Meth.R: a bit less 'not.ok.classes'
53    
54            * R/Tsparse.R (t): generalized "t" method from "dgT*" to "Tsparse*"
55    
56    
57    2006-09-28  Douglas Bates  <bates@R-project.org>
58    
59            * src/dppMatrix.h: Ensure definition of dspMatrix_validate is
60            included.
61    
62            * src/init.c, inst/include/{Matrix.h,Matrix_stubs.h,cholmod.h}:
63            Export C-callable functions used in Zt_create in lme4.
64    
65    2006-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
66    
67            * DESCRIPTION (Version): 0.9975-1
68    
69            * tests/simple.R: less checks fail; using NA, found that our
70                    kronecker() is not base-compatible with NA's.
71    
72            * R/dMatrix.R: "Compare" method now implemented for all cases
73    
74            * R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility
75    
76            * man/dtpMatrix-class.Rd: mention length of 'x' slot
77    
78            * src/dtpMatrix.c (dtpMatrix_validate): fix check
79            * src/dspMatrix.c (dspMatrix_validate): ditto
80    
81            * R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
82              including coercion to [nl]tTMatrix.
83    
84            * R/diagMatrix.R (show): print a header line as for other classes.
85    
86    2006-09-27  Martin Maechler  <maechler@stat.math.ethz.ch>
87    
88            * src/Makefile.win (SUBDIRS): fix typo
89    
90    2006-09-19  Martin Maechler  <maechler@stat.math.ethz.ch>
91    
92            * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
93    
94    2006-09-18  Douglas Bates  <bates@stat.wisc.edu>
95    
96            * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
97            symmetric and y missing in R code using %*% (cholmod_aat doesn't
98            accept a symmetric matrix).
99            * tests/group-methods.R: Uncomment test of crossprod applied to
100            lsCMatrix objects.
101    
102    2006-09-18  Martin Maechler  <maechler@stat.math.ethz.ch>
103    
104            * R/AllClass.R (symmetricMatrix): add validity method (available
105            in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
106    
107            * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
108    
109            * tests/indexing.Rout.save:
110            * tests/indexing.R: additions, mainly for 'lsparse'
111    
112            * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
113            case.
114    
115            * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
116    
117    2006-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
118    
119            * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
120                    as 'N' (1-letter - Ok?)
121    
122            * tests/group-methods.R: add test for logical + NAs
123    
124            * R/dMatrix.R ("Compare"): fix to work with NA's
125    
126            * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
127    
128            * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
129                    which is implemented.
130    
131    2006-09-15  Martin Maechler  <maechler@stat.math.ethz.ch>
132    
133            * src/chm_common.c: coerce logical <-> double instead of
134            typecasting;  needed for "l" matrix handling in cholmod.
135    
136            * tests/other-pkgs.R (graph): small extension in "graph" checks.
137    
138            * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
139            (Tsp2grNEL): other fixes needed
140    
141    2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
142    
143            * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
144                    Matrices, since "lMatrix", also "lsparseM" can have NA
145            * R/ndenseMatrix.R, etc: new source files
146            * man/nsparseMatrix-classes.Rd, etc: new help files
147            * tests/: adaptions
148            * src/chm_common.c (chm_dense_to_SEXP): and others:
149                    new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
150            * src/Csparse.c, etc: ditto
151    
152    2006-09-11  Douglas Bates  <bates@R-project.org>
153    
154            * src/Mutils.[ch],init.c inst/include/*.h: Move the
155            alloc_d**Matrix functions to the lme4 package.
156    
157    2006-09-09  Douglas Bates  <bates@R-project.org>
158    
159            * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
160            fixed
161    
162    2006-09-09  Martin Maechler  <maechler@stat.math.ethz.ch>
163    
164            * R/lMatrix.R: new
165    
166            * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
167    
168            * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
169            * man/tcrossprod.Rd: ditto
170    
171    2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
172    
173            * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
174            for exported functions
175            * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
176            Remove partitioning algorithms for sparse matrix reordering.  The
177            copyright on the Metis code was problematic and the methods were
178            rarely used.
179            * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
180            operations are now done entirely in CHOLMOD code.
181    
182    2006-09-06  Douglas Bates  <bates@R-project.org>
183    
184            * src/Mutils.h: Remove functions that are no longer used.
185    
186    2006-09-04  Douglas Bates  <bates@R-project.org>
187    
188            * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
189            * src/DEPS.mkf: update
190    
191    2006-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>
192    
193            * created branches/Matrix-for-R-2.3.x;  on trunk: do
194            * DESCRIPTION (Version): 0.9975-0
195            (Depends): R (>= 2.4.0)
196    
197    2006-09-01  Douglas Bates  <bates@R-project.org>
198    
199            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
200    
201    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
202    
203            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
204            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
205    
206            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
207    
208    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
209    
210            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
211            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
212            * R/dsparseMatrix.R: ditto
213            * R/Csparse.R: ditto
214    
215    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
216    
217            * R/dMatrix.R (Compare): improve availability of "<", etc
218            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
219    
220    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
221    
222            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
223            of a 0-index which was used as 1-index (..hmm)
224    
225            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
226    
227            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
228            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
229            (.is.diagonal): ditto
230    
231            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
232    
233            * R/Matrix.R (Matrix): also work for NA data
234    
235    2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
236    
237            * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
238            in all cases.
239    
240    2006-08-27  Douglas Bates  <bates@R-project.org>
241    
242            * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
243            (ddense_band): Added triu, tril and band for ddenseMatrix objects.
244    
245    2006-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
246    
247            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
248            subclasses of "ddenseMatrix"
249            * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
250            * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
251            instead of half dozen specialized ones.
252    
253  2006-08-25  Douglas Bates  <bates@R-project.org>  2006-08-25  Douglas Bates  <bates@R-project.org>
254    
255          * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard          * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard

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