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revision 1847, Sat May 19 19:23:28 2007 UTC revision 2020, Wed Aug 1 15:55:52 2007 UTC
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1    2007-08-01 15:44  Douglas Bates <bates@stat.wisc.edu>
2    
3            * [r4686] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
4              src/chm_common.c, src/chm_common.h: Change API for
5              numeric_as_chm_dense and N_AS_CHM_DN
6    
7    2007-08-01  Martin Maechler  <maechler@stat.math.ethz.ch>
8    
9            * src/dtrMatrix.c (dtrMatrix_matrix_mm): fix dimensionality check (!)
10            * tests/matprod.R: regr.test for it
11    
12    2007-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
13    
14            * R/dMatrix.R: fix from Brian for   Math2(., digits = "missing")
15            * tests/group-methods.R: and regression-test it
16    
17    2007-07-19 19:45  Douglas Bates <bates@stat.wisc.edu>
18    
19            * [r4642] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
20              inst/include/cholmod.h, src/chm_common.c, src/init.c: Export
21              triplet_to_sparse, documentation, use typedefs
22    
23    2007-07-18  Martin Maechler  <maechler@stat.math.ethz.ch>
24    
25            * man/dpoMatrix-class.Rd: added 'corMatrix' example
26    
27            * src/dsyMatrix.[ch] (dsyMatrix_as_matrix): new 'keep_dimnames' arg
28            * src/dtrMatrix.[ch] (dtrMatrix_as_matrix): ditto
29            * src/init.c, R/dsyMatrix.R, R/dtrMatrix.R, R/lgTMatrix.R: ditto
30    
31            * R/lsparseMatrix.R: bug fix in "all" method
32            * R/Ops.R (.do.Logic.lsparse): "|" bug in borderline case
33    
34            * R/dsyMatrix.R (coerce->dsTMatrix): (i,j) slots should *not* have names
35            * R/ngTMatrix.R (coerce->ngTMatrix): ditto;
36                    + matrix |-> nMatrix coercion
37            * R/pMatrix.R: + setAs()  to dMatrix and from nMatrix
38            * man/pMatrix-class.Rd: ditto
39    
40            * R/Matrix.R (Summary): method for non-dMatrix
41    
42            * tests/Class+Meth.R (extraValid): new check about "dirty" slots
43            * tests/Class+Meth.R (tstMatrixClass): test norm(.);
44                    test all Summary methods.
45    
46    2007-07-16  Martin Maechler  <maechler@stat.math.ethz.ch>
47    
48            * R/dgeMatrix.R (norm, rcond): methods for 'matrix'
49    
50    2007-07-14  Martin Maechler  <maechler@stat.math.ethz.ch>
51    
52            * R/sparseMatrix.R (norm): simple methods for sparseMatrix
53    
54            * R/pMatrix.R (t?crossprod): methods for pMatrix
55    
56    2007-07-10  Douglas Bates  <bates@stat.wisc.edu>
57    
58            * src/dgeMatrix.c (dgeMatrix_colsums): Get the logic straight.
59    
60    2007-07-09 20:45  Douglas Bates <bates@stat.wisc.edu>
61    
62            * [r4579] src/dgeMatrix.c: Untangle horrible code in dgeMatrix_colsums
63              trying to fix a subtle bug - which has been somewhere else.
64    
65    2007-07-09 19:43  Martin Maechler <maechler@stat.math.ethz.ch>
66    
67            * [r4578] src/dgeMatrix.c: "cleaned" dgeMatrix_colsums() - but did not
68              solve the bug
69    
70    2007-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
71    
72            * src/dgCMatrix.c (compressed_to_TMatrix):
73    
74    2007-07-07  Martin Maechler  <maechler@stat.math.ethz.ch>
75    
76            * src/Csparse.c (Rsparse_validate): new, to have some validity
77            checking for RsparseMatrix
78            * src/dgCMatrix.c (xRMatrix_validate): ditto
79            * src/dtCMatrix.c (tRMatrix_validate): ditto
80    
81    2007-07-07  Douglas Bates <bates@stat.wisc.edu>
82    
83            * [r4567] R/AllClass.R: Slots already in RsparseMatrix were redefined in
84              lgRMatrix
85            * [r4568] DESCRIPTION: Prepare for bug-fix release
86            * [r4570] src/CHOLMOD/Check/cholmod_write.c: Include cholmod_matrixops.h
87              for declaration of cholmod_symmetry
88    
89    2007-07-06  Martin Maechler  <maechler@stat.math.ethz.ch>
90    
91            * DESCRIPTION (Version): 0.999375 merged into the trunk; ready for
92            release.
93    
94    2007-07-06 14:11  Douglas Bates <bates@stat.wisc.edu>
95    
96            * [r4559] src/iohb.c, src/iohb.h: Remove Harwell-Boeing input/output
97              functions - no longer used
98            * [r4560] src/HBMM.c, src/Mutils.c, src/dgTMatrix.c, src/dgeMatrix.c,
99              src/dspMatrix.c, src/dsyMatrix.c, src/dtCMatrix.c,
100              src/factorizations.c, src/sparseQR.c: Replace most calls to Calloc by
101              Alloca
102    
103    2007-07-06 13:14  Martin Maechler <maechler@stat.math.ethz.ch>
104    
105            * [r4558] inst/doc/Comparisons.Rnw, src/CHMfactor.c, src/Csparse.c,
106              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dense.c,
107              src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c, src/sparseQR.c,
108              src/t_gCMatrix_colSums.c: more R_CheckStack()s
109    
110    2007-07-05 18:12  Douglas Bates <bates@stat.wisc.edu>
111    
112            * [r4550] inst/include/Matrix.h: Add the macro N_AS_CHM_DN to "alloca"
113              the required amount of memory then call M_numeric_as_chm_dense.
114            * [r4556] src/Mutils.h, src/dgCMatrix.c: Define and use the Alloca macro
115              (like Calloc but calling alloca)
116    
117    2007-07-05  Martin Maechler  <maechler@stat.math.ethz.ch>
118    
119            * R/sparseMatrix.R (printSpMatrix): renamed from prSpMatrix()
120            and extended with more sophisticated 'col.names' option.
121            * NAMESPACE: export  printSparseMatrix()
122            * man/printSpMatrix.Rd: document, incl. examples
123    
124    2007-07-04 16:21  Douglas Bates <bates@stat.wisc.edu>
125    
126            * [r4543] src/cs_utils.c, src/cs_utils.h, src/dgCMatrix.c,
127              src/dtCMatrix.c, src/sparseQR.c: CSP typedef for *cs and macro
128              AS_CSP. API change - pass the empty structure to Matrix_as_cs.
129    
130    2007-07-04  Martin Maechler  <maechler@stat.math.ethz.ch>
131    
132            * DESCRIPTION (Version): 0.99875-4
133    
134            * tests/Class+Meth.R (tstMatrixClass): add dimnames, and hence test
135            some dimnames perservation.
136    
137            * R/dsTMatrix.R (t-method): keep dimnames
138            * R/dtTMatrix.R:  ditto
139    
140            * R/sparseMatrix.R (prSpMatrix): print colnames when non-trivial
141            and ncol(.) < 10
142    
143            * src/cs_utils.c: drop check_class() and use Matrix_check_class()
144            from Mutils.h
145    
146            * src/lgCMatrix.c ([ln]csc_to_matrix): no longer lose dimnames,
147            e.g. in as(<ngCMatrix>, "matrix")
148    
149    2007-07-01 13:27  Douglas Bates <bates@stat.wisc.edu>
150    
151            * [r4529] .: Create a branch for the API changes from the 0.99875
152              series to the 0.999375 series
153            * [r4530] DESCRIPTION, inst/include/Matrix.h,
154              inst/include/Matrix_stubs.c, src/CHMfactor.c, src/Csparse.c,
155              src/Mutils.h, src/Tsparse.c, src/chm_common.c, src/chm_common.h,
156              src/dense.c, src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c,
157              src/t_gCMatrix_colSums.c: API change - pass the empty structure to the
158              as_cholmod_x functions
159    
160    2007-06-30 09:05  Martin Maechler <maechler@stat.math.ethz.ch>
161    
162            * [r4527] trunk/Matrix/DESCRIPTION, trunk/Matrix/NAMESPACE,
163              trunk/Matrix/inst/doc/Comparisons.Rnw: add session- and hardware-info
164              to Comparisons
165    
166    >>>>>>> .merge-right.r4561
167    2007-06-29  Martin Maechler  <maechler@stat.math.ethz.ch>
168    
169            * DESCRIPTION (Version): 0.99875-3 ready to be released.
170    
171            * R/sparseMatrix.R (spMatrix): make spMatrix(3,4) working
172    
173            * R/AllGeneric.R: set "Math" (and "Math2") group generics in a way
174            that should also work in a future version of R.
175    
176    2007-06-21  Martin Maechler  <maechler@stat.math.ethz.ch>
177    
178            * NAMESPACE, R/AllClass.R: "xsparseVector" class union.
179    
180            * R/sparseVector.R: more *sparseVector coercions, notably for
181            non - double ones.
182    
183    2007-06-19  Martin Maechler  <maechler@stat.math.ethz.ch>
184    
185            * R/colSums.R: new file for all (col|row)(Sums|Means) methods,
186              notably the new ones building on the new .Call(.)s:
187    
188            * src/dgCMatrix.c (DEF_gCMatrix_COLSUMS): use to define
189            all 4 of [dlin]gCMatrix_colSums().
190    
191    2007-06-18 16:12  Douglas Bates <bates@stat.wisc.edu>
192    
193            * [r4472] src/Syms.h, src/init.c: Added Matrix_lengthSym
194            * [r4473] src/dgCMatrix.c: Modified dgCMatrix_colSums for sparseVector
195              result
196    
197    2007-06-16  Martin Maechler  <maechler@stat.math.ethz.ch>
198    
199            * R/kronecker.R: fix typo (could lead to inf.recursion)
200            * test/simple.R: testing that
201    
202            * R/sparseMatrix.R (prSpMatrix): change to be used as print()
203            method as well (which can have arguments, show() can't).
204    
205    2007-06-16 15:52  Douglas Bates <bates@stat.wisc.edu>
206    
207            * [r4466] R/dgCMatrix.R, src/dgCMatrix.c, src/dgCMatrix.h, src/init.c:
208              added dgCMatrix_colSums for [col,row][Sums,Means]
209    
210    2007-06-15 23:15  Douglas Bates <bates@stat.wisc.edu>
211    
212            * [r4460] R/sparseMatrix.R, man/dgCMatrix-class.Rd, src/dgCMatrix.c,
213              src/dgCMatrix.h, src/init.c: added lm.fit.sparse (unexported),
214              coercion of "factor" to "dgCMatrix" and dgCMatrix_cholsol
215            * [r4461] R/AllClass.R, man/sparseMatrix-class.Rd: draft "indicators"
216              class
217            * [r4463] R/sparseMatrix.R, man/dgCMatrix-class.Rd,
218              man/sparseMatrix-class.Rd: Don't need an "indicators" class - use the
219              row names to store the levels - duh!  Added an example.
220    
221    2007-06-14  Martin Maechler  <maechler@stat.math.ethz.ch>
222    
223            * src/Csparse.c (Csparse_validate): check for *repeated* entries
224            thanks to example from Christian Buchta; with a test here:
225            * tests/simple.R:
226    
227    2007-06-07  Martin Maechler  <maechler@stat.math.ethz.ch>
228    
229            * R/Auxiliaries.R (callGeneric): another fix, needed for some cases
230            of colSums(*, sparseResult = TRUE)
231    
232    2007-06-06  Martin Maechler  <maechler@stat.math.ethz.ch>
233    
234            * R/lsparseMatrix.R, R/ldenseMatrix.R (all, any): change default to
235            'na.rm = FALSE' as "everywhere" else in R.
236    
237    2007-06-05 Douglas Bates <bates@stat.wisc.edu>
238    
239            * [r4421] src/CSparse_install.sh: Modify for new organization of
240              CSparse package
241            * [r4425] src/UFsparse_download.sh: Update to version 3.0.0 of
242              SuiteSparse
243            * [r4426] src/Makefile: add ./UFconfig to the include path for
244              compilation
245            * [r4427] src/cs.[ch]: update to CSparse version 2.2.0
246            * [r4428] inst/doc/UFsparse/* src/{AMD,CHOLMOD,COLAMD}/*
247              src/UFconfig/UFconfig.h: Update to version 3.0.0 of SuiteSparse
248    
249    2007-06-05  Martin Maechler  <maechler@stat.math.ethz.ch>
250    
251            * R/Auxiliaries.R (emptyColnames): + argument msg.if.not.empty, used in
252            * R/sparseMatrix.R (prSpMatrix): now gives a message about
253            suppressed column names.
254    
255    2007-06-04 17:13  Douglas Bates <bates@stat.wisc.edu>
256    
257            * [r4418] src/Csparse.c, src/HBMM.c, src/Mutils.c, src/Mutils.h,
258              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dgCMatrix.c,
259              src/dgeMatrix.c, src/dpoMatrix.c, src/dpoMatrix.h, src/dppMatrix.c,
260              src/dppMatrix.h, src/dsCMatrix.c, src/dspMatrix.c, src/dspMatrix.h,
261              src/dsyMatrix.c, src/dsyMatrix.h, src/dtpMatrix.c, src/dtrMatrix.c:
262              Remove warnings after change to const char* CHAR
263    
264    2007-06-04 17:11  Douglas Bates <bates@stat.wisc.edu>
265    
266            * [r4417] inst/include/Matrix_stubs.c, inst/include/cholmod.h: Corrected
267              type of M_cholmod_ssmult
268    
269    2007-06-03 14:42  Douglas Bates <bates@stat.wisc.edu>
270    
271            * [r4412] inst/include/Matrix_stubs.c, inst/include/cholmod.h,
272              src/init.c: Yet another cholmod export - cholmod_ssmult
273    
274    2007-05-23  Martin Maechler  <maechler@stat.math.ethz.ch>
275    
276            * NAMESPACE: exported drop0(), since
277            * man/drop0.Rd: I have seen several cases, I really wanted to use
278            it, so our users may want too.
279    
280    2007-05-22  Martin Maechler  <maechler@stat.math.ethz.ch>
281    
282            * man/colSums.Rd: separately document colSums() etc, since these
283            have the extra argument 'sparseResult'.
284    
285    2007-05-21  Martin Maechler  <maechler@stat.math.ethz.ch>
286    
287            * R/sparseMatrix.R (spMatrix): utility (T)sparse Matrix constructor;
288            * man/spMatrix.Rd: docu., including examples
289    
290            * R/Auxiliaries.R (sp.colMeans): etc, using a patched callGeneric(),
291            in order to make colMeans() etc fast *and* correct.
292            * R/sparseVector.R (replSPvec): "[<-" functionality for
293            sparseVectors; tested in
294            * tests/simple.R:
295    
296    2007-05-19  Martin Maechler  <maechler@stat.math.ethz.ch>
297    
298            * R/sparseMatrix.R (print.sparseSummary): and summary() method for
299            (very) sparse Matrices; output similar to Matlab's print().
300    
301  2007-05-17  Douglas Bates  <bates@stat.wisc.edu>  2007-05-17  Douglas Bates  <bates@stat.wisc.edu>
302    
303          * src/HBMM.c (Matrix_writeMatrixMarket): Write 1-based, not          * src/HBMM.c (Matrix_writeMatrixMarket): Write 1-based, not

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