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revision 2196, Fri May 30 21:49:50 2008 UTC revision 2250, Thu Aug 28 11:54:53 2008 UTC
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1    2008-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * R/Ops.R (Compare(<Csparse>,<Csparse>): fix for nsparseMatrix
4    
5    2008-08-27  Douglas Bates <bates@stat.wisc.edu>
6    
7            * R/sparseMatrix.R: fac2sparse() for NA's
8    
9    2008-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
10    
11            * R/sparseVector.R (all.equal.sparseV): make work for nsparseVector's
12    
13    2008-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
14    
15            * src/dgCMatrix.c (dgCMatrix_LU): partially revert change
16            r2175 (2008-04-23) and do give an error for a singular matrix.
17            * man/lu.Rd, R/Auxiliaries.R (detSparseLU): adapt to that.
18    
19            * R/LU.R: expand( <sparseLU> )
20    
21            * NAMESPACE, man/all.equal-methods.Rd:
22            * R/Matrix.R (all.equal): methods for Matrices,
23            * R/sparseMatrix.R, R/sparseVector.R: sparseMatrices and -Vectors
24    
25    
26    2008-08-23  Douglas Bates <bates@stat.wisc.edu>
27    
28            * [r2243] R/CHMfactor.R, man/CHMfactor-class.Rd: Added expand method and
29              documentation for CHMfactor class
30            * [r2241] R/CHMfactor.R: Added trivial coercion method for CHMfactor ->
31              pMatrix
32    
33    2008-08-19  Martin Maechler  <maechler@stat.math.ethz.ch>
34    
35            * R/nsCMatrix.R (setAs(., dgTMatrix))): remove unused method
36    
37    2008-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
38    
39            * R/Ops.R (.Ops2dge.via.x, and many others): eliminate never-used
40            variable assignments {from "next version" codetools}.
41            * R/Csparse.R, R/Tsparse.R: ditto
42    
43    2008-08-17  Martin Maechler  <maechler@stat.math.ethz.ch>
44    
45            * R/sparseVector.R (sp2vec, coerce to sparseVector):
46            make sure no integer overflows happen, and use double precision
47            (n, index) where appropriate.
48    
49            * tests/Simple.R: test "large" sparse vectors.
50    
51    2008-08-14  Martin Maechler  <maechler@stat.math.ethz.ch>
52    
53            * R/AllClass.R (sparseVector): 'length' and 'i' are "numeric", not
54            just integer (allowing much longer length).
55    
56    2008-07-28  Martin Maechler  <maechler@stat.math.ethz.ch>
57    
58            * R/AllClass.R (diagonalMatrix): extend  "sparseMatrix" instead of
59            "denseMatrix".  This renders "scarceMatrix" dispensable and
60            invalidates part of MM's presentations on "space of Matrix
61            classes", but seems cleaner overall.
62    
63            * R/diagMatrix.R, etc: eliminate "scarceMatrix", replacing it by
64            "sparseMatrix" in method signatures;
65            further, instead of coercing to "sparseMatrix", coerce to
66            "TsparseMatrix" now.
67    
68    2008-07-26  Martin Maechler  <maechler@stat.math.ethz.ch>
69    
70            * src/dgCMatrix.c (dgCMatrix_qrsol): allow third argument 'order' in
71            .Call(.)
72            * R/sparseMatrix.R (lm.fit.sparse), src/dgCMatrix.h, src/init.c: ditto
73    
74    2008-07-24  Martin Maechler  <maechler@stat.math.ethz.ch>
75    
76            * R/dgeMatrix.R: need solve(<dge>, <sparse>) against infinite
77            recursion in new test in
78            * tests/matprod.R: testing the above and another solve() case, below
79    
80            * R/sparseMatrix.R (lm.fit.sparse): slightly more efficient for
81            e.g. triangular 'x'.
82    
83            * src/dgCMatrix.c (dgCMatrix_qrsol): use AS_CSP() hence allowing dtC*
84            * src/dgCMatrix.c (dgCMatrix_cholsol): use AS_CHM_SP() to work
85            correctly with unit-triangular x
86    
87            * src/dsCMatrix.c (dsCMatrix_Csparse_solve): use AS_CHM_SP()
88            instead of not checking diagU.
89    
90            * R/diagMatrix.R, R/Auxiliaries.R: tweaks to allow later
91            experiments where diagonalMatrix would extend sparse*.
92    
93    
94    2008-07-23  Martin Maechler  <maechler@stat.math.ethz.ch>
95    
96            * src/dgCMatrix.c (compressed_non_0_ij): for nnzero(), use
97            "x@p[ncol(x)]" instead of length(x@i).
98            * R/Auxiliaries.R (nnzero): ditto
99    
100            * src/chm_common.c (as_cholmod_sparse): Do not use LENGTH(islot)
101            since that fails for over-allocated i.
102    
103            * tests/validObj.R: more testing of over-allocated (i,x) slots
104    
105    2008-07-23  Martin Maechler  <maechler@stat.math.ethz.ch>
106    
107            * src/chm_common.c (as_cholmod_sparse): Add 4th argument
108            'sort_in_place' and set it to TRUE in call from
109            * src/Csparse.c (Csparse_validate): sort in place, making sure that
110            validObject() continues sort the columns if needed.
111    
112            * tests/validObj.R: now tests that more thoroughly, and
113            * man/CsparseMatrix-class.Rd: documents it.
114    
115    2008-07-22  Douglas Bates <bates@stat.wisc.edu>
116    
117            * [r2233] src/chm_common.c: sort columns more carefully in
118              as_cholmod_sparse
119            * [r2231] src/chm_common.c: check for sorted columns in
120              as_cholmod_sparse instead of assuming it
121            * [r2228] src/cs_utils.c: Use R_alloc for semi-permanent storage when
122              expanding diagonal
123    
124    
125    2008-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
126    
127            * src/cs_utils.c (Matrix_as_cs): add check_Udiag switch
128            * src/cs_utils.h (AS_CSP & AS_CSP__): two versions
129            * src/dtCMatrix.c (dtCMatrix_sparse_solve): no longer needs
130            diagU2N().
131    
132            * R/diagMatrix.R (.sparseDiagonal): new utility, used in "old"
133            .spDiagonal() and new .trDiagonal().
134    
135            * R/dtCMatrix.R (solve): make use of .trDiagonal()
136    
137    2008-07-19  Martin Maechler  <maechler@stat.math.ethz.ch>
138    
139            * R/Auxiliaries.R (dimNamesCheck): fix very long standing buglet,
140            stumbled upon by Michael H.
141    
142            * tests/validObj.R: testing the bug-fix
143    
144            * src/chm_common.h (AS_CHM_SP__, AS_CHM_TR__): the non-diagU2N
145            versions.
146    
147            * src/chm_common.c (as_cholmod_sparse, as_cholmod_triplet): new
148            boolean argument 'check_Udiag' (formerly implicitly was FALSE).
149    
150            * src/Csparse.c (Csparse_Csparse_prod, ...): etc: use the new
151              AS_CHM_SP() which includes diagU2N.
152    
153            * inst/include/Matrix_stubs.c (M_as_cholmod_sparse): similarly
154            adapt to 3 arguments.
155    
156    2008-07-17  Douglas Bates <bates@stat.wisc.edu>
157    
158            * [r2220] src/dtCMatrix.c: Correct number of columns for rhs in
159              dtCMatrix_sparse_solve
160            * [r2219] src/cs_utils.c: eye->nz should be -1 for compressed column
161              storage
162            * [r2217] R/dtCMatrix.R, src/dtCMatrix.c, src/dtCMatrix.h, src/init.c:
163              Replace dtCMatrix_solve by more general dtCMatrix_sparse_solve and add
164              new solve method
165            * [r2216] src/cs_utils.c: Utility csp_eye in case we want to fold
166              Csparse_diagU2N functionality into Matrix_as_cs
167    
168    2008-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
169    
170            * inst/doc/factor2sparse.Rnw: revive a year-old unfinished vignette
171    
172    2008-07-16  Douglas Bates <bates@stat.wisc.edu>
173    
174            * [r2212] R/sparseMatrix.R: fac2sparse gets a drop.unused.levels
175              argument with default TRUE
176            * [r2211] inst/include/Matrix.h, inst/include/Matrix_stubs.c: Export
177              Csparse_diagU2N
178            * [r2210] R/dtCMatrix.R, man/dtCMatrix-class.Rd, src/dtCMatrix.c,
179              src/dtCMatrix.h, src/init.c: Remove vestigial methods based on the
180              parent array; new solve method for signature(a = "dtCMatrix", b =
181              "sparseMatrix")
182    
183    2008-07-14  Martin Maechler  <maechler@stat.math.ethz.ch>
184    
185            * R/diagMatrix.R (.bdiag): also keep result triangular
186    
187    2008-07-13  Douglas Bates <bates@stat.wisc.edu>
188    
189            * [r2208] src/dtCMatrix.c, src/dtTMatrix.c: Revise wording in error
190              messages
191    
192    2008-07-12  Martin Maechler  <maechler@stat.math.ethz.ch>
193    
194            * R/diagMatrix.R (.bdiag): make more sophisticated, keeping
195            symmetric- or nsparse-Matrix, also fixing the bug introduced with
196            the new version (.999375-10).
197    
198            * tests/Simple.R: regression test for the bugs.
199    
200    2008-07-07  Martin Maechler  <maechler@stat.math.ethz.ch>
201    
202            * R/sparseVector.R (spV2M): fix for "isparseVector".
203            Further, fix <diag> -> <sparseVector> coercion
204            (repSpV): add rep(<sparseVector>, .) method
205    
206            * R/sparseMatrix.R ([<-): when the RHS is a "scarce"Matrix, do *not*
207            use as.vector(.).
208    
209            * R/Tsparse.R ([<-): & [CR]sparse.R: methods for value = "sparseVector"
210    
211            * R/AllClass.R: new (hidden) class union "scarceMatrix"
212            * R/AllClass.R: sparseVector: add prototype
213    
214            * src/dsCMatrix.c (chk_nm): fix "Cholesky" check, thanks to
215            Kasper Kristensen
216    
217    2008-06-28  Martin Maechler  <maechler@stat.math.ethz.ch>
218    
219            * tests/other-pkgs.R: add more interesting Matrix -> graph
220    
221    2008-06-27  Martin Maechler  <maechler@stat.math.ethz.ch>
222    
223            * R/sparseMatrix.R (Tsp2grNEL): add 'need.uniq' argument for speed
224            improvement in "[CR]sparseMatrix" -> "graphNEL" coercion.
225    
226    2008-06-25  Martin Maechler  <maechler@stat.math.ethz.ch>
227    
228            * DESCRIPTION: release 0.999375-10 to CRAN
229    
230            * R/diagMatrix.R (.bdiag): use more efficient Bates-algorithm for
231            .bdiag().
232            * man/bdiag.Rd: update, including test.
233    
234    2008-06-24  Martin Maechler  <maechler@stat.math.ethz.ch>
235    
236            * tests/Simple.R: add minimal bdiag() checks
237    
238            * R/diagMatrix.R (bdiag): fix bdiag(diag(4:5)) case;
239              factor out the Tsparse - internal computation into new .bdiag()
240    
241    2008-06-14  Martin Maechler  <maechler@stat.math.ethz.ch>
242    
243            * R/nsparseMatrix.R: specific fast all() and any() methods.
244    
245            * src/dgTMatrix.c (MAKE_gTMatrix_to_geMatrix): better error message
246            when trying to produce too large result.
247    
248            * inst/test-tools.R (checkMatrix): add 'do.matrix' with a check for
249            very large matrices.
250    
251            * R/sparseMatrix.R (printSpMatrix2): new function, used by
252            show(<sparseMatrix>).
253    
254            * R/diagMatrix.R (show): print only diagonal entries when nrow(.) >= 50.
255    
256    2008-06-13  Martin Maechler  <maechler@stat.math.ethz.ch>
257    
258            * src/Mutils.c (m_encodeInd, m_encodeInd2):
259            * R/*.R: .Call(m_encodeInd2?, ..) instead of encodeInd2?(..).
260    
261            * R/Auxiliaries.R (encodeInd2?): care against integer overflow (for
262            big matrices): -> 2nd argument 'di' instead of 'nr' !
263    
264    2008-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
265    
266            * R/dtCMatrix.R: faster dgC* -> dtC* method
267            * tests/Simple.R: (hence removed "FIXME")
268    
269            * R/Auxiliaries.R (copyClass): add 'check = .copyClass.check'
270            which can be be turned off for possible speed gains.
271    
272    2008-06-02  Martin Maechler  <maechler@stat.math.ethz.ch>
273    
274            * R/dMatrix.R, R/Tsparse.R: get rid of some disambiguation warnings
275    
276            * R/not.R: fix !<ldiMatrix>
277            implement two old "FIXME"s:  !<ldenseMatrix> & !<ndenseMatrix>
278    
279            * R/diagMatrix.R (Ops): fix one-off thinko in
280            <diagonal> o <numeric> methods
281    
282            * inst/test-tools.R: checkMatrix(): drop0(m12) unconditionally
283    
284  2008-05-30  Martin Maechler  <maechler@stat.math.ethz.ch>  2008-05-30  Martin Maechler  <maechler@stat.math.ethz.ch>
285    
286          * R/diagMatrix.R (Ops): more <diagonal> o <Matrix> methods          * R/diagMatrix.R (Ops): more <diagonal> o <Matrix> methods

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