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revision 1847, Sat May 19 19:23:28 2007 UTC revision 2061, Sat Sep 1 20:37:11 2007 UTC
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1    2007-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * src/Mutils.h (__sun): clause for alloca.h on Solaris
4    
5    2007-08-16  Martin Maechler  <maechler@stat.math.ethz.ch>
6    
7            * DESCRIPTION (Date, Version): 0.999375-2
8    
9    2007-08-15  Martin Maechler  <maechler@stat.math.ethz.ch>
10    
11            * R/HBMM.R (readMM): make work for pattern matrices as well
12    
13    2007-08-14 13:07  Douglas Bates <bates@stat.wisc.edu>
14    
15            * [r4730] src/Mutils.h: declare alloca
16            * [r4734] NAMESPACE, R/AllGeneric.R, R/Csparse.R, R/HBMM.R, R/Tsparse.R,
17              R/dgCMatrix.R, R/dgTMatrix.R, R/dsCMatrix.R, R/dsTMatrix.R,
18              man/externalFormats.Rd, src/Csparse.c, src/Csparse.h, src/DEPS.mkf,
19              src/HBMM.c, src/HBMM.h, src/Mutils.h, src/SOURCES_C.mkf, src/init.c,
20              src/mmio.c, src/mmio.h: Remove deprecated function writeHB and its
21              methods; switch writeMM to use CHOLMOD code; repair readMM
22    
23    2007-08-14  Martin Maechler  <maechler@stat.math.ethz.ch>
24    
25            * R/nearPD.R, man/nearPD.Rd (nearPD): new function built on Jens
26            Oehlschlaegel's ... result type still to be discussed!
27    
28    2007-08-10  Martin Maechler  <maechler@stat.math.ethz.ch>
29    
30            * man/image-methods.Rd: new, combining all image() methods
31    
32    2007-08-09  Martin Maechler  <maechler@stat.math.ethz.ch>
33    
34            * R/dgCMatrix.R: define qr() and lu() methods for "sparseMatrix"
35            to work via dgC...
36    
37            * R/Matrix.R (Matrix): special treatment for "table" (S3)
38    
39    2007-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
40    
41            * R/dgTMatrix.R (image): change defaults to
42                    aspect = "iso", colorkey = FALSE
43    
44    2007-08-06  Martin Maechler  <maechler@stat.math.ethz.ch>
45    
46            * src/dsyMatrix.c (dsyMatrix_matrix_mm): 'b' might be matrix;
47            must copy its *expanded* x slot before LAPACK call.
48    
49            * tests/matprod.R: test the last days' changes.
50    
51    2007-08-06 16:43  Douglas Bates <bates@stat.wisc.edu>
52    
53            * [r4712] inst/include/Matrix_stubs.c: Change R_cholmod_printf in stubs
54              as well as in sources
55            * [r4713] src/dsyMatrix.c: Duplicate the contents of the RHS before
56              Lapack call
57    
58    2007-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
59    
60            * R/Matrix.R (%*%, crossprod, tcrossprod): add method for
61                    ("Matrix", "matrix") which is needed in some cases.
62            Ditto for solve().
63    
64            * R/colSums.R (.as.dge.Fun): need ddenseMatrix methods to avoid
65            infinite recursion in dispatch for some cases.
66    
67    2007-08-02 08:48  Martin Maechler <maechler@stat.math.ethz.ch>
68    
69            * [r4693] src/chm_common.c: R_cholmod_printf() instead of Rprintf() just
70              so pointers match
71    
72    2007-08-02  Martin Maechler  <maechler@stat.math.ethz.ch>
73    
74            * DESCRIPTION (Date): set ready for release -- 0.999375-1
75    
76    2007-08-01 15:44  Douglas Bates <bates@stat.wisc.edu>
77    
78            * [r4686] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
79              src/chm_common.c, src/chm_common.h: Change API for
80              numeric_as_chm_dense and N_AS_CHM_DN
81    
82    2007-08-01  Martin Maechler  <maechler@stat.math.ethz.ch>
83    
84            * src/dtrMatrix.c (dtrMatrix_matrix_mm): fix dimensionality check (!)
85            * tests/matprod.R: regr.test for it
86    
87    2007-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
88    
89            * R/dMatrix.R: fix from Brian for   Math2(., digits = "missing")
90            * tests/group-methods.R: and regression-test it
91    
92    2007-07-19 19:45  Douglas Bates <bates@stat.wisc.edu>
93    
94            * [r4642] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
95              inst/include/cholmod.h, src/chm_common.c, src/init.c: Export
96              triplet_to_sparse, documentation, use typedefs
97    
98    2007-07-18  Martin Maechler  <maechler@stat.math.ethz.ch>
99    
100            * man/dpoMatrix-class.Rd: added 'corMatrix' example
101    
102            * src/dsyMatrix.[ch] (dsyMatrix_as_matrix): new 'keep_dimnames' arg
103            * src/dtrMatrix.[ch] (dtrMatrix_as_matrix): ditto
104            * src/init.c, R/dsyMatrix.R, R/dtrMatrix.R, R/lgTMatrix.R: ditto
105    
106            * R/lsparseMatrix.R: bug fix in "all" method
107            * R/Ops.R (.do.Logic.lsparse): "|" bug in borderline case
108    
109            * R/dsyMatrix.R (coerce->dsTMatrix): (i,j) slots should *not* have names
110            * R/ngTMatrix.R (coerce->ngTMatrix): ditto;
111                    + matrix |-> nMatrix coercion
112            * R/pMatrix.R: + setAs()  to dMatrix and from nMatrix
113            * man/pMatrix-class.Rd: ditto
114    
115            * R/Matrix.R (Summary): method for non-dMatrix
116    
117            * tests/Class+Meth.R (extraValid): new check about "dirty" slots
118            * tests/Class+Meth.R (tstMatrixClass): test norm(.);
119                    test all Summary methods.
120    
121    2007-07-16  Martin Maechler  <maechler@stat.math.ethz.ch>
122    
123            * R/dgeMatrix.R (norm, rcond): methods for 'matrix'
124    
125    2007-07-14  Martin Maechler  <maechler@stat.math.ethz.ch>
126    
127            * R/sparseMatrix.R (norm): simple methods for sparseMatrix
128    
129            * R/pMatrix.R (t?crossprod): methods for pMatrix
130    
131    2007-07-10  Douglas Bates  <bates@stat.wisc.edu>
132    
133            * src/dgeMatrix.c (dgeMatrix_colsums): Get the logic straight.
134    
135    2007-07-09 20:45  Douglas Bates <bates@stat.wisc.edu>
136    
137            * [r4579] src/dgeMatrix.c: Untangle horrible code in dgeMatrix_colsums
138              trying to fix a subtle bug - which has been somewhere else.
139    
140    2007-07-09 19:43  Martin Maechler <maechler@stat.math.ethz.ch>
141    
142            * [r4578] src/dgeMatrix.c: "cleaned" dgeMatrix_colsums() - but did not
143              solve the bug
144    
145    2007-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
146    
147            * src/dgCMatrix.c (compressed_to_TMatrix):
148    
149    2007-07-07  Martin Maechler  <maechler@stat.math.ethz.ch>
150    
151            * src/Csparse.c (Rsparse_validate): new, to have some validity
152            checking for RsparseMatrix
153            * src/dgCMatrix.c (xRMatrix_validate): ditto
154            * src/dtCMatrix.c (tRMatrix_validate): ditto
155    
156    2007-07-07  Douglas Bates <bates@stat.wisc.edu>
157    
158            * [r4567] R/AllClass.R: Slots already in RsparseMatrix were redefined in
159              lgRMatrix
160            * [r4568] DESCRIPTION: Prepare for bug-fix release
161            * [r4570] src/CHOLMOD/Check/cholmod_write.c: Include cholmod_matrixops.h
162              for declaration of cholmod_symmetry
163    
164    2007-07-06  Martin Maechler  <maechler@stat.math.ethz.ch>
165    
166            * DESCRIPTION (Version): 0.999375 merged into the trunk; ready for
167            release.
168    
169    2007-07-06 14:11  Douglas Bates <bates@stat.wisc.edu>
170    
171            * [r4559] src/iohb.c, src/iohb.h: Remove Harwell-Boeing input/output
172              functions - no longer used
173            * [r4560] src/HBMM.c, src/Mutils.c, src/dgTMatrix.c, src/dgeMatrix.c,
174              src/dspMatrix.c, src/dsyMatrix.c, src/dtCMatrix.c,
175              src/factorizations.c, src/sparseQR.c: Replace most calls to Calloc by
176              Alloca
177    
178    2007-07-06 13:14  Martin Maechler <maechler@stat.math.ethz.ch>
179    
180            * [r4558] inst/doc/Comparisons.Rnw, src/CHMfactor.c, src/Csparse.c,
181              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dense.c,
182              src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c, src/sparseQR.c,
183              src/t_gCMatrix_colSums.c: more R_CheckStack()s
184    
185    2007-07-05 18:12  Douglas Bates <bates@stat.wisc.edu>
186    
187            * [r4550] inst/include/Matrix.h: Add the macro N_AS_CHM_DN to "alloca"
188              the required amount of memory then call M_numeric_as_chm_dense.
189            * [r4556] src/Mutils.h, src/dgCMatrix.c: Define and use the Alloca macro
190              (like Calloc but calling alloca)
191    
192    2007-07-05  Martin Maechler  <maechler@stat.math.ethz.ch>
193    
194            * R/sparseMatrix.R (printSpMatrix): renamed from prSpMatrix()
195            and extended with more sophisticated 'col.names' option.
196            * NAMESPACE: export  printSparseMatrix()
197            * man/printSpMatrix.Rd: document, incl. examples
198    
199    2007-07-04 16:21  Douglas Bates <bates@stat.wisc.edu>
200    
201            * [r4543] src/cs_utils.c, src/cs_utils.h, src/dgCMatrix.c,
202              src/dtCMatrix.c, src/sparseQR.c: CSP typedef for *cs and macro
203              AS_CSP. API change - pass the empty structure to Matrix_as_cs.
204    
205    2007-07-04  Martin Maechler  <maechler@stat.math.ethz.ch>
206    
207            * DESCRIPTION (Version): 0.99875-4
208    
209            * tests/Class+Meth.R (tstMatrixClass): add dimnames, and hence test
210            some dimnames perservation.
211    
212            * R/dsTMatrix.R (t-method): keep dimnames
213            * R/dtTMatrix.R:  ditto
214    
215            * R/sparseMatrix.R (prSpMatrix): print colnames when non-trivial
216            and ncol(.) < 10
217    
218            * src/cs_utils.c: drop check_class() and use Matrix_check_class()
219            from Mutils.h
220    
221            * src/lgCMatrix.c ([ln]csc_to_matrix): no longer lose dimnames,
222            e.g. in as(<ngCMatrix>, "matrix")
223    
224    2007-07-01 13:27  Douglas Bates <bates@stat.wisc.edu>
225    
226            * [r4529] .: Create a branch for the API changes from the 0.99875
227              series to the 0.999375 series
228            * [r4530] DESCRIPTION, inst/include/Matrix.h,
229              inst/include/Matrix_stubs.c, src/CHMfactor.c, src/Csparse.c,
230              src/Mutils.h, src/Tsparse.c, src/chm_common.c, src/chm_common.h,
231              src/dense.c, src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c,
232              src/t_gCMatrix_colSums.c: API change - pass the empty structure to the
233              as_cholmod_x functions
234    
235    2007-06-30 09:05  Martin Maechler <maechler@stat.math.ethz.ch>
236    
237            * [r4527] trunk/Matrix/DESCRIPTION, trunk/Matrix/NAMESPACE,
238              trunk/Matrix/inst/doc/Comparisons.Rnw: add session- and hardware-info
239              to Comparisons
240    
241    >>>>>>> .merge-right.r4561
242    2007-06-29  Martin Maechler  <maechler@stat.math.ethz.ch>
243    
244            * DESCRIPTION (Version): 0.99875-3 ready to be released.
245    
246            * R/sparseMatrix.R (spMatrix): make spMatrix(3,4) working
247    
248            * R/AllGeneric.R: set "Math" (and "Math2") group generics in a way
249            that should also work in a future version of R.
250    
251    2007-06-21  Martin Maechler  <maechler@stat.math.ethz.ch>
252    
253            * NAMESPACE, R/AllClass.R: "xsparseVector" class union.
254    
255            * R/sparseVector.R: more *sparseVector coercions, notably for
256            non - double ones.
257    
258    2007-06-19  Martin Maechler  <maechler@stat.math.ethz.ch>
259    
260            * R/colSums.R: new file for all (col|row)(Sums|Means) methods,
261              notably the new ones building on the new .Call(.)s:
262    
263            * src/dgCMatrix.c (DEF_gCMatrix_COLSUMS): use to define
264            all 4 of [dlin]gCMatrix_colSums().
265    
266    2007-06-18 16:12  Douglas Bates <bates@stat.wisc.edu>
267    
268            * [r4472] src/Syms.h, src/init.c: Added Matrix_lengthSym
269            * [r4473] src/dgCMatrix.c: Modified dgCMatrix_colSums for sparseVector
270              result
271    
272    2007-06-16  Martin Maechler  <maechler@stat.math.ethz.ch>
273    
274            * R/kronecker.R: fix typo (could lead to inf.recursion)
275            * test/simple.R: testing that
276    
277            * R/sparseMatrix.R (prSpMatrix): change to be used as print()
278            method as well (which can have arguments, show() can't).
279    
280    2007-06-16 15:52  Douglas Bates <bates@stat.wisc.edu>
281    
282            * [r4466] R/dgCMatrix.R, src/dgCMatrix.c, src/dgCMatrix.h, src/init.c:
283              added dgCMatrix_colSums for [col,row][Sums,Means]
284    
285    2007-06-15 23:15  Douglas Bates <bates@stat.wisc.edu>
286    
287            * [r4460] R/sparseMatrix.R, man/dgCMatrix-class.Rd, src/dgCMatrix.c,
288              src/dgCMatrix.h, src/init.c: added lm.fit.sparse (unexported),
289              coercion of "factor" to "dgCMatrix" and dgCMatrix_cholsol
290            * [r4461] R/AllClass.R, man/sparseMatrix-class.Rd: draft "indicators"
291              class
292            * [r4463] R/sparseMatrix.R, man/dgCMatrix-class.Rd,
293              man/sparseMatrix-class.Rd: Don't need an "indicators" class - use the
294              row names to store the levels - duh!  Added an example.
295    
296    2007-06-14  Martin Maechler  <maechler@stat.math.ethz.ch>
297    
298            * src/Csparse.c (Csparse_validate): check for *repeated* entries
299            thanks to example from Christian Buchta; with a test here:
300            * tests/simple.R:
301    
302    2007-06-07  Martin Maechler  <maechler@stat.math.ethz.ch>
303    
304            * R/Auxiliaries.R (callGeneric): another fix, needed for some cases
305            of colSums(*, sparseResult = TRUE)
306    
307    2007-06-06  Martin Maechler  <maechler@stat.math.ethz.ch>
308    
309            * R/lsparseMatrix.R, R/ldenseMatrix.R (all, any): change default to
310            'na.rm = FALSE' as "everywhere" else in R.
311    
312    2007-06-05 Douglas Bates <bates@stat.wisc.edu>
313    
314            * [r4421] src/CSparse_install.sh: Modify for new organization of
315              CSparse package
316            * [r4425] src/UFsparse_download.sh: Update to version 3.0.0 of
317              SuiteSparse
318            * [r4426] src/Makefile: add ./UFconfig to the include path for
319              compilation
320            * [r4427] src/cs.[ch]: update to CSparse version 2.2.0
321            * [r4428] inst/doc/UFsparse/* src/{AMD,CHOLMOD,COLAMD}/*
322              src/UFconfig/UFconfig.h: Update to version 3.0.0 of SuiteSparse
323    
324    2007-06-05  Martin Maechler  <maechler@stat.math.ethz.ch>
325    
326            * R/Auxiliaries.R (emptyColnames): + argument msg.if.not.empty, used in
327            * R/sparseMatrix.R (prSpMatrix): now gives a message about
328            suppressed column names.
329    
330    2007-06-04 17:13  Douglas Bates <bates@stat.wisc.edu>
331    
332            * [r4418] src/Csparse.c, src/HBMM.c, src/Mutils.c, src/Mutils.h,
333              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dgCMatrix.c,
334              src/dgeMatrix.c, src/dpoMatrix.c, src/dpoMatrix.h, src/dppMatrix.c,
335              src/dppMatrix.h, src/dsCMatrix.c, src/dspMatrix.c, src/dspMatrix.h,
336              src/dsyMatrix.c, src/dsyMatrix.h, src/dtpMatrix.c, src/dtrMatrix.c:
337              Remove warnings after change to const char* CHAR
338    
339    2007-06-04 17:11  Douglas Bates <bates@stat.wisc.edu>
340    
341            * [r4417] inst/include/Matrix_stubs.c, inst/include/cholmod.h: Corrected
342              type of M_cholmod_ssmult
343    
344    2007-06-03 14:42  Douglas Bates <bates@stat.wisc.edu>
345    
346            * [r4412] inst/include/Matrix_stubs.c, inst/include/cholmod.h,
347              src/init.c: Yet another cholmod export - cholmod_ssmult
348    
349    2007-05-23  Martin Maechler  <maechler@stat.math.ethz.ch>
350    
351            * NAMESPACE: exported drop0(), since
352            * man/drop0.Rd: I have seen several cases, I really wanted to use
353            it, so our users may want too.
354    
355    2007-05-22  Martin Maechler  <maechler@stat.math.ethz.ch>
356    
357            * man/colSums.Rd: separately document colSums() etc, since these
358            have the extra argument 'sparseResult'.
359    
360    2007-05-21  Martin Maechler  <maechler@stat.math.ethz.ch>
361    
362            * R/sparseMatrix.R (spMatrix): utility (T)sparse Matrix constructor;
363            * man/spMatrix.Rd: docu., including examples
364    
365            * R/Auxiliaries.R (sp.colMeans): etc, using a patched callGeneric(),
366            in order to make colMeans() etc fast *and* correct.
367            * R/sparseVector.R (replSPvec): "[<-" functionality for
368            sparseVectors; tested in
369            * tests/simple.R:
370    
371    2007-05-19  Martin Maechler  <maechler@stat.math.ethz.ch>
372    
373            * R/sparseMatrix.R (print.sparseSummary): and summary() method for
374            (very) sparse Matrices; output similar to Matlab's print().
375    
376  2007-05-17  Douglas Bates  <bates@stat.wisc.edu>  2007-05-17  Douglas Bates  <bates@stat.wisc.edu>
377    
378          * src/HBMM.c (Matrix_writeMatrixMarket): Write 1-based, not          * src/HBMM.c (Matrix_writeMatrixMarket): Write 1-based, not

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