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revision 1834, Fri May 11 10:07:17 2007 UTC revision 2051, Tue Aug 14 22:23:53 2007 UTC
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1    2007-08-14 13:07  Douglas Bates <bates@stat.wisc.edu>
2    
3            * [r4730] src/Mutils.h: declare alloca
4            * [r4734] NAMESPACE, R/AllGeneric.R, R/Csparse.R, R/HBMM.R, R/Tsparse.R,
5              R/dgCMatrix.R, R/dgTMatrix.R, R/dsCMatrix.R, R/dsTMatrix.R,
6              man/externalFormats.Rd, src/Csparse.c, src/Csparse.h, src/DEPS.mkf,
7              src/HBMM.c, src/HBMM.h, src/Mutils.h, src/SOURCES_C.mkf, src/init.c,
8              src/mmio.c, src/mmio.h: Remove deprecated function writeHB and its
9              methods; switch writeMM to use CHOLMOD code; repair readMM
10    
11    2007-08-14  Martin Maechler  <maechler@stat.math.ethz.ch>
12    
13            * R/nearPD.R, man/nearPD.Rd (nearPD): new function built on Jens
14            Oehlschlaegel's ... result type still to be discussed!
15    
16    2007-08-10  Martin Maechler  <maechler@stat.math.ethz.ch>
17    
18            * man/image-methods.Rd: new, combining all image() methods
19    
20    2007-08-09  Martin Maechler  <maechler@stat.math.ethz.ch>
21    
22            * R/dgCMatrix.R: define qr() and lu() methods for "sparseMatrix"
23            to work via dgC...
24    
25            * R/Matrix.R (Matrix): special treatment for "table" (S3)
26    
27    2007-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
28    
29            * R/dgTMatrix.R (image): change defaults to
30                    aspect = "iso", colorkey = FALSE
31    
32    2007-08-06  Martin Maechler  <maechler@stat.math.ethz.ch>
33    
34            * src/dsyMatrix.c (dsyMatrix_matrix_mm): 'b' might be matrix;
35            must copy its *expanded* x slot before LAPACK call.
36    
37            * tests/matprod.R: test the last days' changes.
38    
39    2007-08-06 16:43  Douglas Bates <bates@stat.wisc.edu>
40    
41            * [r4712] inst/include/Matrix_stubs.c: Change R_cholmod_printf in stubs
42              as well as in sources
43            * [r4713] src/dsyMatrix.c: Duplicate the contents of the RHS before
44              Lapack call
45    
46    2007-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
47    
48            * R/Matrix.R (%*%, crossprod, tcrossprod): add method for
49                    ("Matrix", "matrix") which is needed in some cases.
50            Ditto for solve().
51    
52            * R/colSums.R (.as.dge.Fun): need ddenseMatrix methods to avoid
53            infinite recursion in dispatch for some cases.
54    
55    2007-08-02 08:48  Martin Maechler <maechler@stat.math.ethz.ch>
56    
57            * [r4693] src/chm_common.c: R_cholmod_printf() instead of Rprintf() just
58              so pointers match
59    
60    2007-08-02  Martin Maechler  <maechler@stat.math.ethz.ch>
61    
62            * DESCRIPTION (Date): set ready for release -- 0.999375-1
63    
64    2007-08-01 15:44  Douglas Bates <bates@stat.wisc.edu>
65    
66            * [r4686] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
67              src/chm_common.c, src/chm_common.h: Change API for
68              numeric_as_chm_dense and N_AS_CHM_DN
69    
70    2007-08-01  Martin Maechler  <maechler@stat.math.ethz.ch>
71    
72            * src/dtrMatrix.c (dtrMatrix_matrix_mm): fix dimensionality check (!)
73            * tests/matprod.R: regr.test for it
74    
75    2007-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
76    
77            * R/dMatrix.R: fix from Brian for   Math2(., digits = "missing")
78            * tests/group-methods.R: and regression-test it
79    
80    2007-07-19 19:45  Douglas Bates <bates@stat.wisc.edu>
81    
82            * [r4642] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
83              inst/include/cholmod.h, src/chm_common.c, src/init.c: Export
84              triplet_to_sparse, documentation, use typedefs
85    
86    2007-07-18  Martin Maechler  <maechler@stat.math.ethz.ch>
87    
88            * man/dpoMatrix-class.Rd: added 'corMatrix' example
89    
90            * src/dsyMatrix.[ch] (dsyMatrix_as_matrix): new 'keep_dimnames' arg
91            * src/dtrMatrix.[ch] (dtrMatrix_as_matrix): ditto
92            * src/init.c, R/dsyMatrix.R, R/dtrMatrix.R, R/lgTMatrix.R: ditto
93    
94            * R/lsparseMatrix.R: bug fix in "all" method
95            * R/Ops.R (.do.Logic.lsparse): "|" bug in borderline case
96    
97            * R/dsyMatrix.R (coerce->dsTMatrix): (i,j) slots should *not* have names
98            * R/ngTMatrix.R (coerce->ngTMatrix): ditto;
99                    + matrix |-> nMatrix coercion
100            * R/pMatrix.R: + setAs()  to dMatrix and from nMatrix
101            * man/pMatrix-class.Rd: ditto
102    
103            * R/Matrix.R (Summary): method for non-dMatrix
104    
105            * tests/Class+Meth.R (extraValid): new check about "dirty" slots
106            * tests/Class+Meth.R (tstMatrixClass): test norm(.);
107                    test all Summary methods.
108    
109    2007-07-16  Martin Maechler  <maechler@stat.math.ethz.ch>
110    
111            * R/dgeMatrix.R (norm, rcond): methods for 'matrix'
112    
113    2007-07-14  Martin Maechler  <maechler@stat.math.ethz.ch>
114    
115            * R/sparseMatrix.R (norm): simple methods for sparseMatrix
116    
117            * R/pMatrix.R (t?crossprod): methods for pMatrix
118    
119    2007-07-10  Douglas Bates  <bates@stat.wisc.edu>
120    
121            * src/dgeMatrix.c (dgeMatrix_colsums): Get the logic straight.
122    
123    2007-07-09 20:45  Douglas Bates <bates@stat.wisc.edu>
124    
125            * [r4579] src/dgeMatrix.c: Untangle horrible code in dgeMatrix_colsums
126              trying to fix a subtle bug - which has been somewhere else.
127    
128    2007-07-09 19:43  Martin Maechler <maechler@stat.math.ethz.ch>
129    
130            * [r4578] src/dgeMatrix.c: "cleaned" dgeMatrix_colsums() - but did not
131              solve the bug
132    
133    2007-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
134    
135            * src/dgCMatrix.c (compressed_to_TMatrix):
136    
137    2007-07-07  Martin Maechler  <maechler@stat.math.ethz.ch>
138    
139            * src/Csparse.c (Rsparse_validate): new, to have some validity
140            checking for RsparseMatrix
141            * src/dgCMatrix.c (xRMatrix_validate): ditto
142            * src/dtCMatrix.c (tRMatrix_validate): ditto
143    
144    2007-07-07  Douglas Bates <bates@stat.wisc.edu>
145    
146            * [r4567] R/AllClass.R: Slots already in RsparseMatrix were redefined in
147              lgRMatrix
148            * [r4568] DESCRIPTION: Prepare for bug-fix release
149            * [r4570] src/CHOLMOD/Check/cholmod_write.c: Include cholmod_matrixops.h
150              for declaration of cholmod_symmetry
151    
152    2007-07-06  Martin Maechler  <maechler@stat.math.ethz.ch>
153    
154            * DESCRIPTION (Version): 0.999375 merged into the trunk; ready for
155            release.
156    
157    2007-07-06 14:11  Douglas Bates <bates@stat.wisc.edu>
158    
159            * [r4559] src/iohb.c, src/iohb.h: Remove Harwell-Boeing input/output
160              functions - no longer used
161            * [r4560] src/HBMM.c, src/Mutils.c, src/dgTMatrix.c, src/dgeMatrix.c,
162              src/dspMatrix.c, src/dsyMatrix.c, src/dtCMatrix.c,
163              src/factorizations.c, src/sparseQR.c: Replace most calls to Calloc by
164              Alloca
165    
166    2007-07-06 13:14  Martin Maechler <maechler@stat.math.ethz.ch>
167    
168            * [r4558] inst/doc/Comparisons.Rnw, src/CHMfactor.c, src/Csparse.c,
169              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dense.c,
170              src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c, src/sparseQR.c,
171              src/t_gCMatrix_colSums.c: more R_CheckStack()s
172    
173    2007-07-05 18:12  Douglas Bates <bates@stat.wisc.edu>
174    
175            * [r4550] inst/include/Matrix.h: Add the macro N_AS_CHM_DN to "alloca"
176              the required amount of memory then call M_numeric_as_chm_dense.
177            * [r4556] src/Mutils.h, src/dgCMatrix.c: Define and use the Alloca macro
178              (like Calloc but calling alloca)
179    
180    2007-07-05  Martin Maechler  <maechler@stat.math.ethz.ch>
181    
182            * R/sparseMatrix.R (printSpMatrix): renamed from prSpMatrix()
183            and extended with more sophisticated 'col.names' option.
184            * NAMESPACE: export  printSparseMatrix()
185            * man/printSpMatrix.Rd: document, incl. examples
186    
187    2007-07-04 16:21  Douglas Bates <bates@stat.wisc.edu>
188    
189            * [r4543] src/cs_utils.c, src/cs_utils.h, src/dgCMatrix.c,
190              src/dtCMatrix.c, src/sparseQR.c: CSP typedef for *cs and macro
191              AS_CSP. API change - pass the empty structure to Matrix_as_cs.
192    
193    2007-07-04  Martin Maechler  <maechler@stat.math.ethz.ch>
194    
195            * DESCRIPTION (Version): 0.99875-4
196    
197            * tests/Class+Meth.R (tstMatrixClass): add dimnames, and hence test
198            some dimnames perservation.
199    
200            * R/dsTMatrix.R (t-method): keep dimnames
201            * R/dtTMatrix.R:  ditto
202    
203            * R/sparseMatrix.R (prSpMatrix): print colnames when non-trivial
204            and ncol(.) < 10
205    
206            * src/cs_utils.c: drop check_class() and use Matrix_check_class()
207            from Mutils.h
208    
209            * src/lgCMatrix.c ([ln]csc_to_matrix): no longer lose dimnames,
210            e.g. in as(<ngCMatrix>, "matrix")
211    
212    2007-07-01 13:27  Douglas Bates <bates@stat.wisc.edu>
213    
214            * [r4529] .: Create a branch for the API changes from the 0.99875
215              series to the 0.999375 series
216            * [r4530] DESCRIPTION, inst/include/Matrix.h,
217              inst/include/Matrix_stubs.c, src/CHMfactor.c, src/Csparse.c,
218              src/Mutils.h, src/Tsparse.c, src/chm_common.c, src/chm_common.h,
219              src/dense.c, src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c,
220              src/t_gCMatrix_colSums.c: API change - pass the empty structure to the
221              as_cholmod_x functions
222    
223    2007-06-30 09:05  Martin Maechler <maechler@stat.math.ethz.ch>
224    
225            * [r4527] trunk/Matrix/DESCRIPTION, trunk/Matrix/NAMESPACE,
226              trunk/Matrix/inst/doc/Comparisons.Rnw: add session- and hardware-info
227              to Comparisons
228    
229    >>>>>>> .merge-right.r4561
230    2007-06-29  Martin Maechler  <maechler@stat.math.ethz.ch>
231    
232            * DESCRIPTION (Version): 0.99875-3 ready to be released.
233    
234            * R/sparseMatrix.R (spMatrix): make spMatrix(3,4) working
235    
236            * R/AllGeneric.R: set "Math" (and "Math2") group generics in a way
237            that should also work in a future version of R.
238    
239    2007-06-21  Martin Maechler  <maechler@stat.math.ethz.ch>
240    
241            * NAMESPACE, R/AllClass.R: "xsparseVector" class union.
242    
243            * R/sparseVector.R: more *sparseVector coercions, notably for
244            non - double ones.
245    
246    2007-06-19  Martin Maechler  <maechler@stat.math.ethz.ch>
247    
248            * R/colSums.R: new file for all (col|row)(Sums|Means) methods,
249              notably the new ones building on the new .Call(.)s:
250    
251            * src/dgCMatrix.c (DEF_gCMatrix_COLSUMS): use to define
252            all 4 of [dlin]gCMatrix_colSums().
253    
254    2007-06-18 16:12  Douglas Bates <bates@stat.wisc.edu>
255    
256            * [r4472] src/Syms.h, src/init.c: Added Matrix_lengthSym
257            * [r4473] src/dgCMatrix.c: Modified dgCMatrix_colSums for sparseVector
258              result
259    
260    2007-06-16  Martin Maechler  <maechler@stat.math.ethz.ch>
261    
262            * R/kronecker.R: fix typo (could lead to inf.recursion)
263            * test/simple.R: testing that
264    
265            * R/sparseMatrix.R (prSpMatrix): change to be used as print()
266            method as well (which can have arguments, show() can't).
267    
268    2007-06-16 15:52  Douglas Bates <bates@stat.wisc.edu>
269    
270            * [r4466] R/dgCMatrix.R, src/dgCMatrix.c, src/dgCMatrix.h, src/init.c:
271              added dgCMatrix_colSums for [col,row][Sums,Means]
272    
273    2007-06-15 23:15  Douglas Bates <bates@stat.wisc.edu>
274    
275            * [r4460] R/sparseMatrix.R, man/dgCMatrix-class.Rd, src/dgCMatrix.c,
276              src/dgCMatrix.h, src/init.c: added lm.fit.sparse (unexported),
277              coercion of "factor" to "dgCMatrix" and dgCMatrix_cholsol
278            * [r4461] R/AllClass.R, man/sparseMatrix-class.Rd: draft "indicators"
279              class
280            * [r4463] R/sparseMatrix.R, man/dgCMatrix-class.Rd,
281              man/sparseMatrix-class.Rd: Don't need an "indicators" class - use the
282              row names to store the levels - duh!  Added an example.
283    
284    2007-06-14  Martin Maechler  <maechler@stat.math.ethz.ch>
285    
286            * src/Csparse.c (Csparse_validate): check for *repeated* entries
287            thanks to example from Christian Buchta; with a test here:
288            * tests/simple.R:
289    
290    2007-06-07  Martin Maechler  <maechler@stat.math.ethz.ch>
291    
292            * R/Auxiliaries.R (callGeneric): another fix, needed for some cases
293            of colSums(*, sparseResult = TRUE)
294    
295    2007-06-06  Martin Maechler  <maechler@stat.math.ethz.ch>
296    
297            * R/lsparseMatrix.R, R/ldenseMatrix.R (all, any): change default to
298            'na.rm = FALSE' as "everywhere" else in R.
299    
300    2007-06-05 Douglas Bates <bates@stat.wisc.edu>
301    
302            * [r4421] src/CSparse_install.sh: Modify for new organization of
303              CSparse package
304            * [r4425] src/UFsparse_download.sh: Update to version 3.0.0 of
305              SuiteSparse
306            * [r4426] src/Makefile: add ./UFconfig to the include path for
307              compilation
308            * [r4427] src/cs.[ch]: update to CSparse version 2.2.0
309            * [r4428] inst/doc/UFsparse/* src/{AMD,CHOLMOD,COLAMD}/*
310              src/UFconfig/UFconfig.h: Update to version 3.0.0 of SuiteSparse
311    
312    2007-06-05  Martin Maechler  <maechler@stat.math.ethz.ch>
313    
314            * R/Auxiliaries.R (emptyColnames): + argument msg.if.not.empty, used in
315            * R/sparseMatrix.R (prSpMatrix): now gives a message about
316            suppressed column names.
317    
318    2007-06-04 17:13  Douglas Bates <bates@stat.wisc.edu>
319    
320            * [r4418] src/Csparse.c, src/HBMM.c, src/Mutils.c, src/Mutils.h,
321              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dgCMatrix.c,
322              src/dgeMatrix.c, src/dpoMatrix.c, src/dpoMatrix.h, src/dppMatrix.c,
323              src/dppMatrix.h, src/dsCMatrix.c, src/dspMatrix.c, src/dspMatrix.h,
324              src/dsyMatrix.c, src/dsyMatrix.h, src/dtpMatrix.c, src/dtrMatrix.c:
325              Remove warnings after change to const char* CHAR
326    
327    2007-06-04 17:11  Douglas Bates <bates@stat.wisc.edu>
328    
329            * [r4417] inst/include/Matrix_stubs.c, inst/include/cholmod.h: Corrected
330              type of M_cholmod_ssmult
331    
332    2007-06-03 14:42  Douglas Bates <bates@stat.wisc.edu>
333    
334            * [r4412] inst/include/Matrix_stubs.c, inst/include/cholmod.h,
335              src/init.c: Yet another cholmod export - cholmod_ssmult
336    
337    2007-05-23  Martin Maechler  <maechler@stat.math.ethz.ch>
338    
339            * NAMESPACE: exported drop0(), since
340            * man/drop0.Rd: I have seen several cases, I really wanted to use
341            it, so our users may want too.
342    
343    2007-05-22  Martin Maechler  <maechler@stat.math.ethz.ch>
344    
345            * man/colSums.Rd: separately document colSums() etc, since these
346            have the extra argument 'sparseResult'.
347    
348    2007-05-21  Martin Maechler  <maechler@stat.math.ethz.ch>
349    
350            * R/sparseMatrix.R (spMatrix): utility (T)sparse Matrix constructor;
351            * man/spMatrix.Rd: docu., including examples
352    
353            * R/Auxiliaries.R (sp.colMeans): etc, using a patched callGeneric(),
354            in order to make colMeans() etc fast *and* correct.
355            * R/sparseVector.R (replSPvec): "[<-" functionality for
356            sparseVectors; tested in
357            * tests/simple.R:
358    
359    2007-05-19  Martin Maechler  <maechler@stat.math.ethz.ch>
360    
361            * R/sparseMatrix.R (print.sparseSummary): and summary() method for
362            (very) sparse Matrices; output similar to Matlab's print().
363    
364    2007-05-17  Douglas Bates  <bates@stat.wisc.edu>
365    
366            * src/HBMM.c (Matrix_writeMatrixMarket): Write 1-based, not
367            0-based, indices (Jose Quesada <quesada@gmail.com>).
368    
369    2007-05-16  Douglas Bates  <bates@stat.wisc.edu>
370    
371            * R/CHMfactor.R: Added solve methods for a CHMfactor object.
372    
373    2007-05-16  Martin Maechler  <maechler@stat.math.ethz.ch>
374    
375            * R/Auxiliaries.R (sparsapply): new utility, much faster than
376            tapply1() for large sparse matrices.
377    
378    2007-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
379    
380            * R/Matrix.R (dim<-): reshape now via sparseVector.
381    
382            * R/sparseVector.R: methods and function for
383            * R/AllClass.R: new "sparseVector" class and daughters.
384            * NAMESPACE: export new classes
385    
386    2007-05-14  Martin Maechler  <maechler@stat.math.ethz.ch>
387    
388            * DESCRIPTION (Version): 0.99875-1
389            * src/Makefile.win: also remove Lapack code from here (cf. 04-25).
390    
391  2007-05-11  Martin Maechler  <maechler@stat.math.ethz.ch>  2007-05-11  Martin Maechler  <maechler@stat.math.ethz.ch>
392    
393          * R/Tsparse.R ([, Tsparse): fix last case: *duplicated*, symmetric          * R/Tsparse.R ([, Tsparse): fix last case: *duplicated*, symmetric

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