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revision 1827, Wed Apr 25 22:22:41 2007 UTC revision 1960, Fri Jul 6 16:54:43 2007 UTC
# Line 1  Line 1 
1    2007-07-06 14:11  Douglas Bates <bates@stat.wisc.edu>
2    
3            * [r4559] src/iohb.c, src/iohb.h: Remove Harwell-Boeing input/output
4              functions - no longer used
5            * [r4560] src/HBMM.c, src/Mutils.c, src/dgTMatrix.c, src/dgeMatrix.c,
6              src/dspMatrix.c, src/dsyMatrix.c, src/dtCMatrix.c,
7              src/factorizations.c, src/sparseQR.c: Replace most calls to Calloc by
8              Alloca
9    
10    2007-07-06 13:14  Martin Maechler <maechler@stat.math.ethz.ch>
11    
12            * [r4558] inst/doc/Comparisons.Rnw, src/CHMfactor.c, src/Csparse.c,
13              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dense.c,
14              src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c, src/sparseQR.c,
15              src/t_gCMatrix_colSums.c: more R_CheckStack()s
16    
17    2007-07-05 18:12  Douglas Bates <bates@stat.wisc.edu>
18    
19            * [r4550] inst/include/Matrix.h: Add the macro N_AS_CHM_DN to "alloca"
20              the required amount of memory then call M_numeric_as_chm_dense.
21            * [r4556] src/Mutils.h, src/dgCMatrix.c: Define and use the Alloca macro
22              (like Calloc but calling alloca)
23    
24    2007-07-05  Martin Maechler  <maechler@stat.math.ethz.ch>
25    
26            * R/sparseMatrix.R (printSpMatrix): renamed from prSpMatrix()
27            and extended with more sophisticated 'col.names' option.
28            * NAMESPACE: export  printSparseMatrix()
29            * man/printSpMatrix.Rd: document, incl. examples
30    
31    2007-07-04 16:21  Douglas Bates <bates@stat.wisc.edu>
32    
33            * [r4543] src/cs_utils.c, src/cs_utils.h, src/dgCMatrix.c,
34              src/dtCMatrix.c, src/sparseQR.c: CSP typedef for *cs and macro
35              AS_CSP. API change - pass the empty structure to Matrix_as_cs.
36    
37    2007-07-04  Martin Maechler  <maechler@stat.math.ethz.ch>
38    
39            * DESCRIPTION (Version): 0.99875-4
40    
41            * tests/Class+Meth.R (tstMatrixClass): add dimnames, and hence test
42            some dimnames perservation.
43    
44            * R/dsTMatrix.R (t-method): keep dimnames
45            * R/dtTMatrix.R:  ditto
46    
47            * R/sparseMatrix.R (prSpMatrix): print colnames when non-trivial
48            and ncol(.) < 10
49    
50            * src/cs_utils.c: drop check_class() and use Matrix_check_class()
51            from Mutils.h
52    
53            * src/lgCMatrix.c ([ln]csc_to_matrix): no longer lose dimnames,
54            e.g. in as(<ngCMatrix>, "matrix")
55    
56    2007-07-01 13:27  Douglas Bates <bates@stat.wisc.edu>
57    
58            * [r4529] .: Create a branch for the API changes from the 0.99875
59              series to the 0.999375 series
60            * [r4530] DESCRIPTION, inst/include/Matrix.h,
61              inst/include/Matrix_stubs.c, src/CHMfactor.c, src/Csparse.c,
62              src/Mutils.h, src/Tsparse.c, src/chm_common.c, src/chm_common.h,
63              src/dense.c, src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c,
64              src/t_gCMatrix_colSums.c: API change - pass the empty structure to the
65              as_cholmod_x functions
66    
67    2007-06-30 09:05  Martin Maechler <maechler@stat.math.ethz.ch>
68    
69            * [r4527] trunk/Matrix/DESCRIPTION, trunk/Matrix/NAMESPACE,
70              trunk/Matrix/inst/doc/Comparisons.Rnw: add session- and hardware-info
71              to Comparisons
72    
73    >>>>>>> .merge-right.r4561
74    2007-06-29  Martin Maechler  <maechler@stat.math.ethz.ch>
75    
76            * DESCRIPTION (Version): 0.99875-3 ready to be released.
77    
78            * R/sparseMatrix.R (spMatrix): make spMatrix(3,4) working
79    
80            * R/AllGeneric.R: set "Math" (and "Math2") group generics in a way
81            that should also work in a future version of R.
82    
83    2007-06-21  Martin Maechler  <maechler@stat.math.ethz.ch>
84    
85            * NAMESPACE, R/AllClass.R: "xsparseVector" class union.
86    
87            * R/sparseVector.R: more *sparseVector coercions, notably for
88            non - double ones.
89    
90    2007-06-19  Martin Maechler  <maechler@stat.math.ethz.ch>
91    
92            * R/colSums.R: new file for all (col|row)(Sums|Means) methods,
93              notably the new ones building on the new .Call(.)s:
94    
95            * src/dgCMatrix.c (DEF_gCMatrix_COLSUMS): use to define
96            all 4 of [dlin]gCMatrix_colSums().
97    
98    2007-06-18 16:12  Douglas Bates <bates@stat.wisc.edu>
99    
100            * [r4472] src/Syms.h, src/init.c: Added Matrix_lengthSym
101            * [r4473] src/dgCMatrix.c: Modified dgCMatrix_colSums for sparseVector
102              result
103    
104    2007-06-16  Martin Maechler  <maechler@stat.math.ethz.ch>
105    
106            * R/kronecker.R: fix typo (could lead to inf.recursion)
107            * test/simple.R: testing that
108    
109            * R/sparseMatrix.R (prSpMatrix): change to be used as print()
110            method as well (which can have arguments, show() can't).
111    
112    2007-06-16 15:52  Douglas Bates <bates@stat.wisc.edu>
113    
114            * [r4466] R/dgCMatrix.R, src/dgCMatrix.c, src/dgCMatrix.h, src/init.c:
115              added dgCMatrix_colSums for [col,row][Sums,Means]
116    
117    2007-06-15 23:15  Douglas Bates <bates@stat.wisc.edu>
118    
119            * [r4460] R/sparseMatrix.R, man/dgCMatrix-class.Rd, src/dgCMatrix.c,
120              src/dgCMatrix.h, src/init.c: added lm.fit.sparse (unexported),
121              coercion of "factor" to "dgCMatrix" and dgCMatrix_cholsol
122            * [r4461] R/AllClass.R, man/sparseMatrix-class.Rd: draft "indicators"
123              class
124            * [r4463] R/sparseMatrix.R, man/dgCMatrix-class.Rd,
125              man/sparseMatrix-class.Rd: Don't need an "indicators" class - use the
126              row names to store the levels - duh!  Added an example.
127    
128    2007-06-14  Martin Maechler  <maechler@stat.math.ethz.ch>
129    
130            * src/Csparse.c (Csparse_validate): check for *repeated* entries
131            thanks to example from Christian Buchta; with a test here:
132            * tests/simple.R:
133    
134    2007-06-07  Martin Maechler  <maechler@stat.math.ethz.ch>
135    
136            * R/Auxiliaries.R (callGeneric): another fix, needed for some cases
137            of colSums(*, sparseResult = TRUE)
138    
139    2007-06-06  Martin Maechler  <maechler@stat.math.ethz.ch>
140    
141            * R/lsparseMatrix.R, R/ldenseMatrix.R (all, any): change default to
142            'na.rm = FALSE' as "everywhere" else in R.
143    
144    2007-06-05 Douglas Bates <bates@stat.wisc.edu>
145    
146            * [r4421] src/CSparse_install.sh: Modify for new organization of
147              CSparse package
148            * [r4425] src/UFsparse_download.sh: Update to version 3.0.0 of
149              SuiteSparse
150            * [r4426] src/Makefile: add ./UFconfig to the include path for
151              compilation
152            * [r4427] src/cs.[ch]: update to CSparse version 2.2.0
153            * [r4428] inst/doc/UFsparse/* src/{AMD,CHOLMOD,COLAMD}/*
154              src/UFconfig/UFconfig.h: Update to version 3.0.0 of SuiteSparse
155    
156    2007-06-05  Martin Maechler  <maechler@stat.math.ethz.ch>
157    
158            * R/Auxiliaries.R (emptyColnames): + argument msg.if.not.empty, used in
159            * R/sparseMatrix.R (prSpMatrix): now gives a message about
160            suppressed column names.
161    
162    2007-06-04 17:13  Douglas Bates <bates@stat.wisc.edu>
163    
164            * [r4418] src/Csparse.c, src/HBMM.c, src/Mutils.c, src/Mutils.h,
165              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dgCMatrix.c,
166              src/dgeMatrix.c, src/dpoMatrix.c, src/dpoMatrix.h, src/dppMatrix.c,
167              src/dppMatrix.h, src/dsCMatrix.c, src/dspMatrix.c, src/dspMatrix.h,
168              src/dsyMatrix.c, src/dsyMatrix.h, src/dtpMatrix.c, src/dtrMatrix.c:
169              Remove warnings after change to const char* CHAR
170    
171    2007-06-04 17:11  Douglas Bates <bates@stat.wisc.edu>
172    
173            * [r4417] inst/include/Matrix_stubs.c, inst/include/cholmod.h: Corrected
174              type of M_cholmod_ssmult
175    
176    2007-06-03 14:42  Douglas Bates <bates@stat.wisc.edu>
177    
178            * [r4412] inst/include/Matrix_stubs.c, inst/include/cholmod.h,
179              src/init.c: Yet another cholmod export - cholmod_ssmult
180    
181    2007-05-23  Martin Maechler  <maechler@stat.math.ethz.ch>
182    
183            * NAMESPACE: exported drop0(), since
184            * man/drop0.Rd: I have seen several cases, I really wanted to use
185            it, so our users may want too.
186    
187    2007-05-22  Martin Maechler  <maechler@stat.math.ethz.ch>
188    
189            * man/colSums.Rd: separately document colSums() etc, since these
190            have the extra argument 'sparseResult'.
191    
192    2007-05-21  Martin Maechler  <maechler@stat.math.ethz.ch>
193    
194            * R/sparseMatrix.R (spMatrix): utility (T)sparse Matrix constructor;
195            * man/spMatrix.Rd: docu., including examples
196    
197            * R/Auxiliaries.R (sp.colMeans): etc, using a patched callGeneric(),
198            in order to make colMeans() etc fast *and* correct.
199            * R/sparseVector.R (replSPvec): "[<-" functionality for
200            sparseVectors; tested in
201            * tests/simple.R:
202    
203    2007-05-19  Martin Maechler  <maechler@stat.math.ethz.ch>
204    
205            * R/sparseMatrix.R (print.sparseSummary): and summary() method for
206            (very) sparse Matrices; output similar to Matlab's print().
207    
208    2007-05-17  Douglas Bates  <bates@stat.wisc.edu>
209    
210            * src/HBMM.c (Matrix_writeMatrixMarket): Write 1-based, not
211            0-based, indices (Jose Quesada <quesada@gmail.com>).
212    
213    2007-05-16  Douglas Bates  <bates@stat.wisc.edu>
214    
215            * R/CHMfactor.R: Added solve methods for a CHMfactor object.
216    
217    2007-05-16  Martin Maechler  <maechler@stat.math.ethz.ch>
218    
219            * R/Auxiliaries.R (sparsapply): new utility, much faster than
220            tapply1() for large sparse matrices.
221    
222    2007-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
223    
224            * R/Matrix.R (dim<-): reshape now via sparseVector.
225    
226            * R/sparseVector.R: methods and function for
227            * R/AllClass.R: new "sparseVector" class and daughters.
228            * NAMESPACE: export new classes
229    
230    2007-05-14  Martin Maechler  <maechler@stat.math.ethz.ch>
231    
232            * DESCRIPTION (Version): 0.99875-1
233            * src/Makefile.win: also remove Lapack code from here (cf. 04-25).
234    
235    2007-05-11  Martin Maechler  <maechler@stat.math.ethz.ch>
236    
237            * R/Tsparse.R ([, Tsparse): fix last case: *duplicated*, symmetric
238            indexing
239            * tests/indexing.R: test set for that.
240    
241    2007-05-08  Martin Maechler  <maechler@stat.math.ethz.ch>
242    
243            * R/Tsparse.R (replTmat): fix the case of *duplicated* index
244            entries.
245            * tests/indexing.R(out): add regression test for it
246    
247    2007-04-30  Martin Maechler  <maechler@stat.math.ethz.ch>
248    
249            * R/(l(dense|sparse))?Matrix.R (!): use 'x', not 'e1' as argument
250            name for "!" method definitions.
251    
252    2007-04-26  Martin Maechler  <maechler@stat.math.ethz.ch>
253    
254            * R/Tsparse.R (intI): new utility, used for "[" :
255                    Cleanup up there, and fixes for duplicated indices - more TODO!
256    
257            * tests/indexing.R(out): more tests
258    
259  2007-04-25  Douglas Bates  <bates@stat.wisc.edu>  2007-04-25  Douglas Bates  <bates@stat.wisc.edu>
260    
261          * DESCRIPTION,src/Makefile: require R>= 2.5.0 and remove Lapack          * DESCRIPTION,src/Makefile: require R>= 2.5.0 and remove Lapack
# Line 6  Line 264 
264          * src/init.c,inst/include/{Matrix_stubs.c,cholmod.h}:export          * src/init.c,inst/include/{Matrix_stubs.c,cholmod.h}:export
265          cholmod_factorize_p (used in lme4 for GLMMs and NLMMs).          cholmod_factorize_p (used in lme4 for GLMMs and NLMMs).
266    
267    2007-04-21  Martin Maechler  <maechler@stat.math.ethz.ch>
268    
269            * R/Matrix.R (image): method for all Matrices, not just sparse ones.
270    
271    2007-04-17  Martin Maechler  <maechler@stat.math.ethz.ch>
272    
273            * R/Auxiliaries.R (tapply1): unname(.) -> colSums() etc don't end
274            up with extraneous names '0'...'<n-1>'
275    
276  2007-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>  2007-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
277    
278          * R/dgTMatrix.R (mat2dgT): care about NAs          * R/dgTMatrix.R (mat2dgT): care about NAs

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