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revision 1847, Sat May 19 19:23:28 2007 UTC revision 2008, Thu Jul 19 19:47:59 2007 UTC
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1    2007-07-19 19:45  Douglas Bates <bates@stat.wisc.edu>
2    
3            * [r4642] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
4              inst/include/cholmod.h, src/chm_common.c, src/init.c: Export
5              triplet_to_sparse, documentation, use typedefs
6    
7    2007-07-18  Martin Maechler  <maechler@stat.math.ethz.ch>
8    
9            * man/dpoMatrix-class.Rd: added 'corMatrix' example
10    
11            * src/dsyMatrix.[ch] (dsyMatrix_as_matrix): new 'keep_dimnames' arg
12            * src/dtrMatrix.[ch] (dtrMatrix_as_matrix): ditto
13            * src/init.c, R/dsyMatrix.R, R/dtrMatrix.R, R/lgTMatrix.R: ditto
14    
15            * R/lsparseMatrix.R: bug fix in "all" method
16            * R/Ops.R (.do.Logic.lsparse): "|" bug in borderline case
17    
18            * R/dsyMatrix.R (coerce->dsTMatrix): (i,j) slots should *not* have names
19            * R/ngTMatrix.R (coerce->ngTMatrix): ditto;
20                    + matrix |-> nMatrix coercion
21            * R/pMatrix.R: + setAs()  to dMatrix and from nMatrix
22            * man/pMatrix-class.Rd: ditto
23    
24            * R/Matrix.R (Summary): method for non-dMatrix
25    
26            * tests/Class+Meth.R (extraValid): new check about "dirty" slots
27            * tests/Class+Meth.R (tstMatrixClass): test norm(.);
28                    test all Summary methods.
29    
30    2007-07-16  Martin Maechler  <maechler@stat.math.ethz.ch>
31    
32            * R/dgeMatrix.R (norm, rcond): methods for 'matrix'
33    
34    2007-07-14  Martin Maechler  <maechler@stat.math.ethz.ch>
35    
36            * R/sparseMatrix.R (norm): simple methods for sparseMatrix
37    
38            * R/pMatrix.R (t?crossprod): methods for pMatrix
39    
40    2007-07-10  Douglas Bates  <bates@stat.wisc.edu>
41    
42            * src/dgeMatrix.c (dgeMatrix_colsums): Get the logic straight.
43    
44    2007-07-09 20:45  Douglas Bates <bates@stat.wisc.edu>
45    
46            * [r4579] src/dgeMatrix.c: Untangle horrible code in dgeMatrix_colsums
47              trying to fix a subtle bug - which has been somewhere else.
48    
49    2007-07-09 19:43  Martin Maechler <maechler@stat.math.ethz.ch>
50    
51            * [r4578] src/dgeMatrix.c: "cleaned" dgeMatrix_colsums() - but did not
52              solve the bug
53    
54    2007-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
55    
56            * src/dgCMatrix.c (compressed_to_TMatrix):
57    
58    2007-07-07  Martin Maechler  <maechler@stat.math.ethz.ch>
59    
60            * src/Csparse.c (Rsparse_validate): new, to have some validity
61            checking for RsparseMatrix
62            * src/dgCMatrix.c (xRMatrix_validate): ditto
63            * src/dtCMatrix.c (tRMatrix_validate): ditto
64    
65    2007-07-07  Douglas Bates <bates@stat.wisc.edu>
66    
67            * [r4567] R/AllClass.R: Slots already in RsparseMatrix were redefined in
68              lgRMatrix
69            * [r4568] DESCRIPTION: Prepare for bug-fix release
70            * [r4570] src/CHOLMOD/Check/cholmod_write.c: Include cholmod_matrixops.h
71              for declaration of cholmod_symmetry
72    
73    2007-07-06  Martin Maechler  <maechler@stat.math.ethz.ch>
74    
75            * DESCRIPTION (Version): 0.999375 merged into the trunk; ready for
76            release.
77    
78    2007-07-06 14:11  Douglas Bates <bates@stat.wisc.edu>
79    
80            * [r4559] src/iohb.c, src/iohb.h: Remove Harwell-Boeing input/output
81              functions - no longer used
82            * [r4560] src/HBMM.c, src/Mutils.c, src/dgTMatrix.c, src/dgeMatrix.c,
83              src/dspMatrix.c, src/dsyMatrix.c, src/dtCMatrix.c,
84              src/factorizations.c, src/sparseQR.c: Replace most calls to Calloc by
85              Alloca
86    
87    2007-07-06 13:14  Martin Maechler <maechler@stat.math.ethz.ch>
88    
89            * [r4558] inst/doc/Comparisons.Rnw, src/CHMfactor.c, src/Csparse.c,
90              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dense.c,
91              src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c, src/sparseQR.c,
92              src/t_gCMatrix_colSums.c: more R_CheckStack()s
93    
94    2007-07-05 18:12  Douglas Bates <bates@stat.wisc.edu>
95    
96            * [r4550] inst/include/Matrix.h: Add the macro N_AS_CHM_DN to "alloca"
97              the required amount of memory then call M_numeric_as_chm_dense.
98            * [r4556] src/Mutils.h, src/dgCMatrix.c: Define and use the Alloca macro
99              (like Calloc but calling alloca)
100    
101    2007-07-05  Martin Maechler  <maechler@stat.math.ethz.ch>
102    
103            * R/sparseMatrix.R (printSpMatrix): renamed from prSpMatrix()
104            and extended with more sophisticated 'col.names' option.
105            * NAMESPACE: export  printSparseMatrix()
106            * man/printSpMatrix.Rd: document, incl. examples
107    
108    2007-07-04 16:21  Douglas Bates <bates@stat.wisc.edu>
109    
110            * [r4543] src/cs_utils.c, src/cs_utils.h, src/dgCMatrix.c,
111              src/dtCMatrix.c, src/sparseQR.c: CSP typedef for *cs and macro
112              AS_CSP. API change - pass the empty structure to Matrix_as_cs.
113    
114    2007-07-04  Martin Maechler  <maechler@stat.math.ethz.ch>
115    
116            * DESCRIPTION (Version): 0.99875-4
117    
118            * tests/Class+Meth.R (tstMatrixClass): add dimnames, and hence test
119            some dimnames perservation.
120    
121            * R/dsTMatrix.R (t-method): keep dimnames
122            * R/dtTMatrix.R:  ditto
123    
124            * R/sparseMatrix.R (prSpMatrix): print colnames when non-trivial
125            and ncol(.) < 10
126    
127            * src/cs_utils.c: drop check_class() and use Matrix_check_class()
128            from Mutils.h
129    
130            * src/lgCMatrix.c ([ln]csc_to_matrix): no longer lose dimnames,
131            e.g. in as(<ngCMatrix>, "matrix")
132    
133    2007-07-01 13:27  Douglas Bates <bates@stat.wisc.edu>
134    
135            * [r4529] .: Create a branch for the API changes from the 0.99875
136              series to the 0.999375 series
137            * [r4530] DESCRIPTION, inst/include/Matrix.h,
138              inst/include/Matrix_stubs.c, src/CHMfactor.c, src/Csparse.c,
139              src/Mutils.h, src/Tsparse.c, src/chm_common.c, src/chm_common.h,
140              src/dense.c, src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c,
141              src/t_gCMatrix_colSums.c: API change - pass the empty structure to the
142              as_cholmod_x functions
143    
144    2007-06-30 09:05  Martin Maechler <maechler@stat.math.ethz.ch>
145    
146            * [r4527] trunk/Matrix/DESCRIPTION, trunk/Matrix/NAMESPACE,
147              trunk/Matrix/inst/doc/Comparisons.Rnw: add session- and hardware-info
148              to Comparisons
149    
150    >>>>>>> .merge-right.r4561
151    2007-06-29  Martin Maechler  <maechler@stat.math.ethz.ch>
152    
153            * DESCRIPTION (Version): 0.99875-3 ready to be released.
154    
155            * R/sparseMatrix.R (spMatrix): make spMatrix(3,4) working
156    
157            * R/AllGeneric.R: set "Math" (and "Math2") group generics in a way
158            that should also work in a future version of R.
159    
160    2007-06-21  Martin Maechler  <maechler@stat.math.ethz.ch>
161    
162            * NAMESPACE, R/AllClass.R: "xsparseVector" class union.
163    
164            * R/sparseVector.R: more *sparseVector coercions, notably for
165            non - double ones.
166    
167    2007-06-19  Martin Maechler  <maechler@stat.math.ethz.ch>
168    
169            * R/colSums.R: new file for all (col|row)(Sums|Means) methods,
170              notably the new ones building on the new .Call(.)s:
171    
172            * src/dgCMatrix.c (DEF_gCMatrix_COLSUMS): use to define
173            all 4 of [dlin]gCMatrix_colSums().
174    
175    2007-06-18 16:12  Douglas Bates <bates@stat.wisc.edu>
176    
177            * [r4472] src/Syms.h, src/init.c: Added Matrix_lengthSym
178            * [r4473] src/dgCMatrix.c: Modified dgCMatrix_colSums for sparseVector
179              result
180    
181    2007-06-16  Martin Maechler  <maechler@stat.math.ethz.ch>
182    
183            * R/kronecker.R: fix typo (could lead to inf.recursion)
184            * test/simple.R: testing that
185    
186            * R/sparseMatrix.R (prSpMatrix): change to be used as print()
187            method as well (which can have arguments, show() can't).
188    
189    2007-06-16 15:52  Douglas Bates <bates@stat.wisc.edu>
190    
191            * [r4466] R/dgCMatrix.R, src/dgCMatrix.c, src/dgCMatrix.h, src/init.c:
192              added dgCMatrix_colSums for [col,row][Sums,Means]
193    
194    2007-06-15 23:15  Douglas Bates <bates@stat.wisc.edu>
195    
196            * [r4460] R/sparseMatrix.R, man/dgCMatrix-class.Rd, src/dgCMatrix.c,
197              src/dgCMatrix.h, src/init.c: added lm.fit.sparse (unexported),
198              coercion of "factor" to "dgCMatrix" and dgCMatrix_cholsol
199            * [r4461] R/AllClass.R, man/sparseMatrix-class.Rd: draft "indicators"
200              class
201            * [r4463] R/sparseMatrix.R, man/dgCMatrix-class.Rd,
202              man/sparseMatrix-class.Rd: Don't need an "indicators" class - use the
203              row names to store the levels - duh!  Added an example.
204    
205    2007-06-14  Martin Maechler  <maechler@stat.math.ethz.ch>
206    
207            * src/Csparse.c (Csparse_validate): check for *repeated* entries
208            thanks to example from Christian Buchta; with a test here:
209            * tests/simple.R:
210    
211    2007-06-07  Martin Maechler  <maechler@stat.math.ethz.ch>
212    
213            * R/Auxiliaries.R (callGeneric): another fix, needed for some cases
214            of colSums(*, sparseResult = TRUE)
215    
216    2007-06-06  Martin Maechler  <maechler@stat.math.ethz.ch>
217    
218            * R/lsparseMatrix.R, R/ldenseMatrix.R (all, any): change default to
219            'na.rm = FALSE' as "everywhere" else in R.
220    
221    2007-06-05 Douglas Bates <bates@stat.wisc.edu>
222    
223            * [r4421] src/CSparse_install.sh: Modify for new organization of
224              CSparse package
225            * [r4425] src/UFsparse_download.sh: Update to version 3.0.0 of
226              SuiteSparse
227            * [r4426] src/Makefile: add ./UFconfig to the include path for
228              compilation
229            * [r4427] src/cs.[ch]: update to CSparse version 2.2.0
230            * [r4428] inst/doc/UFsparse/* src/{AMD,CHOLMOD,COLAMD}/*
231              src/UFconfig/UFconfig.h: Update to version 3.0.0 of SuiteSparse
232    
233    2007-06-05  Martin Maechler  <maechler@stat.math.ethz.ch>
234    
235            * R/Auxiliaries.R (emptyColnames): + argument msg.if.not.empty, used in
236            * R/sparseMatrix.R (prSpMatrix): now gives a message about
237            suppressed column names.
238    
239    2007-06-04 17:13  Douglas Bates <bates@stat.wisc.edu>
240    
241            * [r4418] src/Csparse.c, src/HBMM.c, src/Mutils.c, src/Mutils.h,
242              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dgCMatrix.c,
243              src/dgeMatrix.c, src/dpoMatrix.c, src/dpoMatrix.h, src/dppMatrix.c,
244              src/dppMatrix.h, src/dsCMatrix.c, src/dspMatrix.c, src/dspMatrix.h,
245              src/dsyMatrix.c, src/dsyMatrix.h, src/dtpMatrix.c, src/dtrMatrix.c:
246              Remove warnings after change to const char* CHAR
247    
248    2007-06-04 17:11  Douglas Bates <bates@stat.wisc.edu>
249    
250            * [r4417] inst/include/Matrix_stubs.c, inst/include/cholmod.h: Corrected
251              type of M_cholmod_ssmult
252    
253    2007-06-03 14:42  Douglas Bates <bates@stat.wisc.edu>
254    
255            * [r4412] inst/include/Matrix_stubs.c, inst/include/cholmod.h,
256              src/init.c: Yet another cholmod export - cholmod_ssmult
257    
258    2007-05-23  Martin Maechler  <maechler@stat.math.ethz.ch>
259    
260            * NAMESPACE: exported drop0(), since
261            * man/drop0.Rd: I have seen several cases, I really wanted to use
262            it, so our users may want too.
263    
264    2007-05-22  Martin Maechler  <maechler@stat.math.ethz.ch>
265    
266            * man/colSums.Rd: separately document colSums() etc, since these
267            have the extra argument 'sparseResult'.
268    
269    2007-05-21  Martin Maechler  <maechler@stat.math.ethz.ch>
270    
271            * R/sparseMatrix.R (spMatrix): utility (T)sparse Matrix constructor;
272            * man/spMatrix.Rd: docu., including examples
273    
274            * R/Auxiliaries.R (sp.colMeans): etc, using a patched callGeneric(),
275            in order to make colMeans() etc fast *and* correct.
276            * R/sparseVector.R (replSPvec): "[<-" functionality for
277            sparseVectors; tested in
278            * tests/simple.R:
279    
280    2007-05-19  Martin Maechler  <maechler@stat.math.ethz.ch>
281    
282            * R/sparseMatrix.R (print.sparseSummary): and summary() method for
283            (very) sparse Matrices; output similar to Matlab's print().
284    
285  2007-05-17  Douglas Bates  <bates@stat.wisc.edu>  2007-05-17  Douglas Bates  <bates@stat.wisc.edu>
286    
287          * src/HBMM.c (Matrix_writeMatrixMarket): Write 1-based, not          * src/HBMM.c (Matrix_writeMatrixMarket): Write 1-based, not

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