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revision 1932, Fri Jun 29 16:43:47 2007 UTC revision 2106, Wed Jan 23 09:36:04 2008 UTC
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1    2008-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * tests/factorizing.R (checkSchur): and more tests for checking Schur()
4    
5            * inst/test-tools.R (isOrthogonal): new function; also re-sort file structure
6    
7    2008-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
8    
9            * R/ngTMatrix.R: allow as(<numeric matrix>, "ngTMatrix") and hence
10            coercion to "nMatrix" and "pMatrix"
11    
12            * R/AllClass.R: "Schur" class;  "number" class union
13            * man/number-class.Rd:
14            * man/Schur-class.Rd:
15    
16            * R/eigen.R (.dgeSchur): utility, and return "Schur" class
17            (.simpleSchur): Schur() method for diagonal matrices
18            (.triSchur):    Schur() method for triangular matrices
19            (Schur.sym):    Schur() for symmetric matrices {building on eigen()}.
20    
21    
22    2008-01-21  Martin Maechler  <maechler@stat.math.ethz.ch>
23    
24            * src/dgCMatrix.c (dgCMatrix_QR): set @Dim slot (as per doc)
25    
26    2008-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
27    
28            * R/CHMfactor.R (solve): method for b="numeric", but also b="ANY"
29                    in order to ensure 'system = *' is not lost;
30                    formals()$system instead of cut&paste.
31            * tests/factorizing.R: test solve(<CHM..>, <numeric>)
32    
33    2008-01-11  Martin Maechler  <maechler@stat.math.ethz.ch>
34    
35            * DESCRIPTION (Date): make ready for release --> 0.999375-4
36    
37            * R/dgeMatrix.R: fix rcond() method for "dgeMatrix".
38    
39    2007-12-08  Martin Maechler  <maechler@stat.math.ethz.ch>
40    
41            * R/pMatrix.R: as(*, "matrix") now returns 0/1 *integer* matrix,
42                    and hence does as.vector(.).
43            * man/pMatrix-class.Rd: docs
44            * R/sparseMatrix.R: fix for printing "integer sparse"
45    
46            * tests/Class+Meth.R (tstMatrixClass): test M[FALSE], M[2] etc
47    
48            * R/Matrix.R and others: use "exact" function argument list for
49                    both "["   : (x, i,j, ..., drop)
50                    and  "[<-" : (x, i,j, ..., value)
51    
52            * R/denseMatrix.R: M[i] and M[i] <- v  (i vector) now work
53            * R/Tsparse.R (replTmat):    ditto
54            * R/diagMatrix.R (replDiag): ditto
55            * R/Csparse.R (replCmat):    ditto {was it worth the pain?}
56            * tests/indexing.R: testing the above
57    
58    2007-12-07  Martin Maechler  <maechler@stat.math.ethz.ch>
59    
60            * R/sparseMatrix.R (cov2cor): method for sparse matrices
61    
62            * R/diagMatrix.R ([<-): fix   D[ cbind(i,j) ] <- v
63    
64            * R/bind2.R: fix for Rsparse* and rbind2(dense,dense)
65    
66            * tests/Class+Meth.R: test cbind2, rbind2  and  diag<-
67    
68    2007-12-06  Martin Maechler  <maechler@stat.math.ethz.ch>
69    
70            * R/Matrix.R: "generic" cov2cor() method
71    
72            * R/nearPD.R: new 'only.values', 'keepDiag' arguments;
73                    speed up Q %*% D %*% t(Q)
74            * tests/dpoMatrix.R: test nearPD()
75    
76    2007-12-05  Doug Bates and Martin Maechler
77    
78            * R/sparseMatrix.R: xtabs(*, sparse=.) function; an extention of
79            stats::xtabs() allowing to create sparse matrices.
80    
81    2007-10-08  Martin Maechler  <maechler@stat.math.ethz.ch>
82    
83            * DESCRIPTION (Version): *-4 (released *-3 two days ago)
84    
85    2007-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
86    
87            * R/pMatrix.R: solve(<Matrix>, <pMatrix>)
88    
89    2007-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
90    
91            * R/LU.R: solve() method for "denseLU"
92    
93    2007-10-01  Martin Maechler  <maechler@stat.math.ethz.ch>
94    
95            * DESCRIPTION (Version): 0.999375-3 preparing for release
96    
97            * R/AllGeneric.R: simplify  if(.) .. else .. for R <= 2.5.1
98    
99            * R/Matrix.R (Matrix): .Internal(matrix(..)) different for R >= 2.7.0
100    
101    2007-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
102    
103            * R/pMatrix.R (.m.mult.pMat): fix <matrix> %*% <pMatrix>,
104              thanks to Kasper Kristensen.
105            * tests/matprod.R: regression test for that.
106    
107    2007-09-23 17:32  Douglas Bates <bates@stat.wisc.edu>
108    
109            * [r4778] R/AllGeneric.R: Check R version before defining generics for
110              primitives
111    
112    2007-09-13  Martin Maechler  <maechler@stat.math.ethz.ch>
113    
114            * R/denseMatrix.R (rcond): method
115            * R/sparseQR.R (rcond): method, use x or t(x)
116    
117    2007-09-12  Martin Maechler  <maechler@stat.math.ethz.ch>
118    
119            * R/dgeMatrix.R (rcond): method: work via qr.R() for non-square
120            matrices.
121            * R/sparseMatrix.R: Ditto for all other rcond() method definitions.
122    
123            * man/rcond.Rd: mention the more general definition, and add
124            example for non-square matrices.
125    
126            * man/chol.Rd: new file, for the S4 chol() generic and all methods.
127    
128    2007-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
129    
130            * R/sparseQR.R: add qr.R() method [to be used for rcond()]
131    
132    2007-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
133    
134            * R/Matrix.R ([<-): add (Matrix,missing,ANY,Matrix) etc
135            * tests/indexing.R: add new regression for the above cases.
136    
137    2007-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
138    
139            * src/Mutils.h (__sun): clause for alloca.h on Solaris
140    
141    2007-08-16  Martin Maechler  <maechler@stat.math.ethz.ch>
142    
143            * DESCRIPTION (Date, Version): 0.999375-2
144    
145    2007-08-15  Martin Maechler  <maechler@stat.math.ethz.ch>
146    
147            * R/HBMM.R (readMM): make work for pattern matrices as well
148    
149    2007-08-14 13:07  Douglas Bates <bates@stat.wisc.edu>
150    
151            * [r4730] src/Mutils.h: declare alloca
152            * [r4734] NAMESPACE, R/AllGeneric.R, R/Csparse.R, R/HBMM.R, R/Tsparse.R,
153              R/dgCMatrix.R, R/dgTMatrix.R, R/dsCMatrix.R, R/dsTMatrix.R,
154              man/externalFormats.Rd, src/Csparse.c, src/Csparse.h, src/DEPS.mkf,
155              src/HBMM.c, src/HBMM.h, src/Mutils.h, src/SOURCES_C.mkf, src/init.c,
156              src/mmio.c, src/mmio.h: Remove deprecated function writeHB and its
157              methods; switch writeMM to use CHOLMOD code; repair readMM
158    
159    2007-08-14  Martin Maechler  <maechler@stat.math.ethz.ch>
160    
161            * R/nearPD.R, man/nearPD.Rd (nearPD): new function built on Jens
162            Oehlschlaegel's ... result type still to be discussed!
163    
164    2007-08-10  Martin Maechler  <maechler@stat.math.ethz.ch>
165    
166            * man/image-methods.Rd: new, combining all image() methods
167    
168    2007-08-09  Martin Maechler  <maechler@stat.math.ethz.ch>
169    
170            * R/dgCMatrix.R: define qr() and lu() methods for "sparseMatrix"
171            to work via dgC...
172    
173            * R/Matrix.R (Matrix): special treatment for "table" (S3)
174    
175    2007-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
176    
177            * R/dgTMatrix.R (image): change defaults to
178                    aspect = "iso", colorkey = FALSE
179    
180    2007-08-06  Martin Maechler  <maechler@stat.math.ethz.ch>
181    
182            * src/dsyMatrix.c (dsyMatrix_matrix_mm): 'b' might be matrix;
183            must copy its *expanded* x slot before LAPACK call.
184    
185            * tests/matprod.R: test the last days' changes.
186    
187    2007-08-06 16:43  Douglas Bates <bates@stat.wisc.edu>
188    
189            * [r4712] inst/include/Matrix_stubs.c: Change R_cholmod_printf in stubs
190              as well as in sources
191            * [r4713] src/dsyMatrix.c: Duplicate the contents of the RHS before
192              Lapack call
193    
194    2007-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
195    
196            * R/Matrix.R (%*%, crossprod, tcrossprod): add method for
197                    ("Matrix", "matrix") which is needed in some cases.
198            Ditto for solve().
199    
200            * R/colSums.R (.as.dge.Fun): need ddenseMatrix methods to avoid
201            infinite recursion in dispatch for some cases.
202    
203    2007-08-02 08:48  Martin Maechler <maechler@stat.math.ethz.ch>
204    
205            * [r4693] src/chm_common.c: R_cholmod_printf() instead of Rprintf() just
206              so pointers match
207    
208    2007-08-02  Martin Maechler  <maechler@stat.math.ethz.ch>
209    
210            * DESCRIPTION (Date): set ready for release -- 0.999375-1
211    
212    2007-08-01 15:44  Douglas Bates <bates@stat.wisc.edu>
213    
214            * [r4686] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
215              src/chm_common.c, src/chm_common.h: Change API for
216              numeric_as_chm_dense and N_AS_CHM_DN
217    
218    2007-08-01  Martin Maechler  <maechler@stat.math.ethz.ch>
219    
220            * src/dtrMatrix.c (dtrMatrix_matrix_mm): fix dimensionality check (!)
221            * tests/matprod.R: regr.test for it
222    
223    2007-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
224    
225            * R/dMatrix.R: fix from Brian for   Math2(., digits = "missing")
226            * tests/group-methods.R: and regression-test it
227    
228    2007-07-19 19:45  Douglas Bates <bates@stat.wisc.edu>
229    
230            * [r4642] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
231              inst/include/cholmod.h, src/chm_common.c, src/init.c: Export
232              triplet_to_sparse, documentation, use typedefs
233    
234    2007-07-18  Martin Maechler  <maechler@stat.math.ethz.ch>
235    
236            * man/dpoMatrix-class.Rd: added 'corMatrix' example
237    
238            * src/dsyMatrix.[ch] (dsyMatrix_as_matrix): new 'keep_dimnames' arg
239            * src/dtrMatrix.[ch] (dtrMatrix_as_matrix): ditto
240            * src/init.c, R/dsyMatrix.R, R/dtrMatrix.R, R/lgTMatrix.R: ditto
241    
242            * R/lsparseMatrix.R: bug fix in "all" method
243            * R/Ops.R (.do.Logic.lsparse): "|" bug in borderline case
244    
245            * R/dsyMatrix.R (coerce->dsTMatrix): (i,j) slots should *not* have names
246            * R/ngTMatrix.R (coerce->ngTMatrix): ditto;
247                    + matrix |-> nMatrix coercion
248            * R/pMatrix.R: + setAs()  to dMatrix and from nMatrix
249            * man/pMatrix-class.Rd: ditto
250    
251            * R/Matrix.R (Summary): method for non-dMatrix
252    
253            * tests/Class+Meth.R (extraValid): new check about "dirty" slots
254            * tests/Class+Meth.R (tstMatrixClass): test norm(.);
255                    test all Summary methods.
256    
257    2007-07-16  Martin Maechler  <maechler@stat.math.ethz.ch>
258    
259            * R/dgeMatrix.R (norm, rcond): methods for 'matrix'
260    
261    2007-07-14  Martin Maechler  <maechler@stat.math.ethz.ch>
262    
263            * R/sparseMatrix.R (norm): simple methods for sparseMatrix
264    
265            * R/pMatrix.R (t?crossprod): methods for pMatrix
266    
267    2007-07-10  Douglas Bates  <bates@stat.wisc.edu>
268    
269            * src/dgeMatrix.c (dgeMatrix_colsums): Get the logic straight.
270    
271    2007-07-09 20:45  Douglas Bates <bates@stat.wisc.edu>
272    
273            * [r4579] src/dgeMatrix.c: Untangle horrible code in dgeMatrix_colsums
274              trying to fix a subtle bug - which has been somewhere else.
275    
276    2007-07-09 19:43  Martin Maechler <maechler@stat.math.ethz.ch>
277    
278            * [r4578] src/dgeMatrix.c: "cleaned" dgeMatrix_colsums() - but did not
279              solve the bug
280    
281    2007-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
282    
283            * src/dgCMatrix.c (compressed_to_TMatrix):
284    
285    2007-07-07  Martin Maechler  <maechler@stat.math.ethz.ch>
286    
287            * src/Csparse.c (Rsparse_validate): new, to have some validity
288            checking for RsparseMatrix
289            * src/dgCMatrix.c (xRMatrix_validate): ditto
290            * src/dtCMatrix.c (tRMatrix_validate): ditto
291    
292    2007-07-07  Douglas Bates <bates@stat.wisc.edu>
293    
294            * [r4567] R/AllClass.R: Slots already in RsparseMatrix were redefined in
295              lgRMatrix
296            * [r4568] DESCRIPTION: Prepare for bug-fix release
297            * [r4570] src/CHOLMOD/Check/cholmod_write.c: Include cholmod_matrixops.h
298              for declaration of cholmod_symmetry
299    
300    2007-07-06  Martin Maechler  <maechler@stat.math.ethz.ch>
301    
302            * DESCRIPTION (Version): 0.999375 merged into the trunk; ready for
303            release.
304    
305    2007-07-06 14:11  Douglas Bates <bates@stat.wisc.edu>
306    
307            * [r4559] src/iohb.c, src/iohb.h: Remove Harwell-Boeing input/output
308              functions - no longer used
309            * [r4560] src/HBMM.c, src/Mutils.c, src/dgTMatrix.c, src/dgeMatrix.c,
310              src/dspMatrix.c, src/dsyMatrix.c, src/dtCMatrix.c,
311              src/factorizations.c, src/sparseQR.c: Replace most calls to Calloc by
312              Alloca
313    
314    2007-07-06 13:14  Martin Maechler <maechler@stat.math.ethz.ch>
315    
316            * [r4558] inst/doc/Comparisons.Rnw, src/CHMfactor.c, src/Csparse.c,
317              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dense.c,
318              src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c, src/sparseQR.c,
319              src/t_gCMatrix_colSums.c: more R_CheckStack()s
320    
321    2007-07-05 18:12  Douglas Bates <bates@stat.wisc.edu>
322    
323            * [r4550] inst/include/Matrix.h: Add the macro N_AS_CHM_DN to "alloca"
324              the required amount of memory then call M_numeric_as_chm_dense.
325            * [r4556] src/Mutils.h, src/dgCMatrix.c: Define and use the Alloca macro
326              (like Calloc but calling alloca)
327    
328    2007-07-05  Martin Maechler  <maechler@stat.math.ethz.ch>
329    
330            * R/sparseMatrix.R (printSpMatrix): renamed from prSpMatrix()
331            and extended with more sophisticated 'col.names' option.
332            * NAMESPACE: export  printSparseMatrix()
333            * man/printSpMatrix.Rd: document, incl. examples
334    
335    2007-07-04 16:21  Douglas Bates <bates@stat.wisc.edu>
336    
337            * [r4543] src/cs_utils.c, src/cs_utils.h, src/dgCMatrix.c,
338              src/dtCMatrix.c, src/sparseQR.c: CSP typedef for *cs and macro
339              AS_CSP. API change - pass the empty structure to Matrix_as_cs.
340    
341    2007-07-04  Martin Maechler  <maechler@stat.math.ethz.ch>
342    
343            * DESCRIPTION (Version): 0.99875-4
344    
345            * tests/Class+Meth.R (tstMatrixClass): add dimnames, and hence test
346            some dimnames perservation.
347    
348            * R/dsTMatrix.R (t-method): keep dimnames
349            * R/dtTMatrix.R:  ditto
350    
351            * R/sparseMatrix.R (prSpMatrix): print colnames when non-trivial
352            and ncol(.) < 10
353    
354            * src/cs_utils.c: drop check_class() and use Matrix_check_class()
355            from Mutils.h
356    
357            * src/lgCMatrix.c ([ln]csc_to_matrix): no longer lose dimnames,
358            e.g. in as(<ngCMatrix>, "matrix")
359    
360    2007-07-01 13:27  Douglas Bates <bates@stat.wisc.edu>
361    
362            * [r4529] .: Create a branch for the API changes from the 0.99875
363              series to the 0.999375 series
364            * [r4530] DESCRIPTION, inst/include/Matrix.h,
365              inst/include/Matrix_stubs.c, src/CHMfactor.c, src/Csparse.c,
366              src/Mutils.h, src/Tsparse.c, src/chm_common.c, src/chm_common.h,
367              src/dense.c, src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c,
368              src/t_gCMatrix_colSums.c: API change - pass the empty structure to the
369              as_cholmod_x functions
370    
371    2007-06-30 09:05  Martin Maechler <maechler@stat.math.ethz.ch>
372    
373            * [r4527] trunk/Matrix/DESCRIPTION, trunk/Matrix/NAMESPACE,
374              trunk/Matrix/inst/doc/Comparisons.Rnw: add session- and hardware-info
375              to Comparisons
376    
377    >>>>>>> .merge-right.r4561
378  2007-06-29  Martin Maechler  <maechler@stat.math.ethz.ch>  2007-06-29  Martin Maechler  <maechler@stat.math.ethz.ch>
379    
380          * DESCRIPTION (Version): 0.99875-3 ready to be released.          * DESCRIPTION (Version): 0.99875-3 ready to be released.

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