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revision 1903, Sat Jun 16 18:31:51 2007 UTC revision 2105, Tue Jan 15 10:16:29 2008 UTC
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1    2008-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * R/CHMfactor.R (solve): method for b="numeric", but also b="ANY"
4                    in order to ensure 'system = *' is not lost;
5                    formals()$system instead of cut&paste.
6            * tests/factorizing.R: test solve(<CHM..>, <numeric>)
7    
8    2008-01-11  Martin Maechler  <maechler@stat.math.ethz.ch>
9    
10            * DESCRIPTION (Date): make ready for release --> 0.999375-4
11    
12            * R/dgeMatrix.R: fix rcond() method for "dgeMatrix".
13    
14    2007-12-08  Martin Maechler  <maechler@stat.math.ethz.ch>
15    
16            * R/pMatrix.R: as(*, "matrix") now returns 0/1 *integer* matrix,
17                    and hence does as.vector(.).
18            * man/pMatrix-class.Rd: docs
19            * R/sparseMatrix.R: fix for printing "integer sparse"
20    
21            * tests/Class+Meth.R (tstMatrixClass): test M[FALSE], M[2] etc
22    
23            * R/Matrix.R and others: use "exact" function argument list for
24                    both "["   : (x, i,j, ..., drop)
25                    and  "[<-" : (x, i,j, ..., value)
26    
27            * R/denseMatrix.R: M[i] and M[i] <- v  (i vector) now work
28            * R/Tsparse.R (replTmat):    ditto
29            * R/diagMatrix.R (replDiag): ditto
30            * R/Csparse.R (replCmat):    ditto {was it worth the pain?}
31            * tests/indexing.R: testing the above
32    
33    2007-12-07  Martin Maechler  <maechler@stat.math.ethz.ch>
34    
35            * R/sparseMatrix.R (cov2cor): method for sparse matrices
36    
37            * R/diagMatrix.R ([<-): fix   D[ cbind(i,j) ] <- v
38    
39            * R/bind2.R: fix for Rsparse* and rbind2(dense,dense)
40    
41            * tests/Class+Meth.R: test cbind2, rbind2  and  diag<-
42    
43    2007-12-06  Martin Maechler  <maechler@stat.math.ethz.ch>
44    
45            * R/Matrix.R: "generic" cov2cor() method
46    
47            * R/nearPD.R: new 'only.values', 'keepDiag' arguments;
48                    speed up Q %*% D %*% t(Q)
49            * tests/dpoMatrix.R: test nearPD()
50    
51    2007-12-05  Doug Bates and Martin Maechler
52    
53            * R/sparseMatrix.R: xtabs(*, sparse=.) function; an extention of
54            stats::xtabs() allowing to create sparse matrices.
55    
56    2007-10-08  Martin Maechler  <maechler@stat.math.ethz.ch>
57    
58            * DESCRIPTION (Version): *-4 (released *-3 two days ago)
59    
60    2007-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
61    
62            * R/pMatrix.R: solve(<Matrix>, <pMatrix>)
63    
64    2007-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
65    
66            * R/LU.R: solve() method for "denseLU"
67    
68    2007-10-01  Martin Maechler  <maechler@stat.math.ethz.ch>
69    
70            * DESCRIPTION (Version): 0.999375-3 preparing for release
71    
72            * R/AllGeneric.R: simplify  if(.) .. else .. for R <= 2.5.1
73    
74            * R/Matrix.R (Matrix): .Internal(matrix(..)) different for R >= 2.7.0
75    
76    2007-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
77    
78            * R/pMatrix.R (.m.mult.pMat): fix <matrix> %*% <pMatrix>,
79              thanks to Kasper Kristensen.
80            * tests/matprod.R: regression test for that.
81    
82    2007-09-23 17:32  Douglas Bates <bates@stat.wisc.edu>
83    
84            * [r4778] R/AllGeneric.R: Check R version before defining generics for
85              primitives
86    
87    2007-09-13  Martin Maechler  <maechler@stat.math.ethz.ch>
88    
89            * R/denseMatrix.R (rcond): method
90            * R/sparseQR.R (rcond): method, use x or t(x)
91    
92    2007-09-12  Martin Maechler  <maechler@stat.math.ethz.ch>
93    
94            * R/dgeMatrix.R (rcond): method: work via qr.R() for non-square
95            matrices.
96            * R/sparseMatrix.R: Ditto for all other rcond() method definitions.
97    
98            * man/rcond.Rd: mention the more general definition, and add
99            example for non-square matrices.
100    
101            * man/chol.Rd: new file, for the S4 chol() generic and all methods.
102    
103    2007-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
104    
105            * R/sparseQR.R: add qr.R() method [to be used for rcond()]
106    
107    2007-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
108    
109            * R/Matrix.R ([<-): add (Matrix,missing,ANY,Matrix) etc
110            * tests/indexing.R: add new regression for the above cases.
111    
112    2007-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
113    
114            * src/Mutils.h (__sun): clause for alloca.h on Solaris
115    
116    2007-08-16  Martin Maechler  <maechler@stat.math.ethz.ch>
117    
118            * DESCRIPTION (Date, Version): 0.999375-2
119    
120    2007-08-15  Martin Maechler  <maechler@stat.math.ethz.ch>
121    
122            * R/HBMM.R (readMM): make work for pattern matrices as well
123    
124    2007-08-14 13:07  Douglas Bates <bates@stat.wisc.edu>
125    
126            * [r4730] src/Mutils.h: declare alloca
127            * [r4734] NAMESPACE, R/AllGeneric.R, R/Csparse.R, R/HBMM.R, R/Tsparse.R,
128              R/dgCMatrix.R, R/dgTMatrix.R, R/dsCMatrix.R, R/dsTMatrix.R,
129              man/externalFormats.Rd, src/Csparse.c, src/Csparse.h, src/DEPS.mkf,
130              src/HBMM.c, src/HBMM.h, src/Mutils.h, src/SOURCES_C.mkf, src/init.c,
131              src/mmio.c, src/mmio.h: Remove deprecated function writeHB and its
132              methods; switch writeMM to use CHOLMOD code; repair readMM
133    
134    2007-08-14  Martin Maechler  <maechler@stat.math.ethz.ch>
135    
136            * R/nearPD.R, man/nearPD.Rd (nearPD): new function built on Jens
137            Oehlschlaegel's ... result type still to be discussed!
138    
139    2007-08-10  Martin Maechler  <maechler@stat.math.ethz.ch>
140    
141            * man/image-methods.Rd: new, combining all image() methods
142    
143    2007-08-09  Martin Maechler  <maechler@stat.math.ethz.ch>
144    
145            * R/dgCMatrix.R: define qr() and lu() methods for "sparseMatrix"
146            to work via dgC...
147    
148            * R/Matrix.R (Matrix): special treatment for "table" (S3)
149    
150    2007-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
151    
152            * R/dgTMatrix.R (image): change defaults to
153                    aspect = "iso", colorkey = FALSE
154    
155    2007-08-06  Martin Maechler  <maechler@stat.math.ethz.ch>
156    
157            * src/dsyMatrix.c (dsyMatrix_matrix_mm): 'b' might be matrix;
158            must copy its *expanded* x slot before LAPACK call.
159    
160            * tests/matprod.R: test the last days' changes.
161    
162    2007-08-06 16:43  Douglas Bates <bates@stat.wisc.edu>
163    
164            * [r4712] inst/include/Matrix_stubs.c: Change R_cholmod_printf in stubs
165              as well as in sources
166            * [r4713] src/dsyMatrix.c: Duplicate the contents of the RHS before
167              Lapack call
168    
169    2007-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
170    
171            * R/Matrix.R (%*%, crossprod, tcrossprod): add method for
172                    ("Matrix", "matrix") which is needed in some cases.
173            Ditto for solve().
174    
175            * R/colSums.R (.as.dge.Fun): need ddenseMatrix methods to avoid
176            infinite recursion in dispatch for some cases.
177    
178    2007-08-02 08:48  Martin Maechler <maechler@stat.math.ethz.ch>
179    
180            * [r4693] src/chm_common.c: R_cholmod_printf() instead of Rprintf() just
181              so pointers match
182    
183    2007-08-02  Martin Maechler  <maechler@stat.math.ethz.ch>
184    
185            * DESCRIPTION (Date): set ready for release -- 0.999375-1
186    
187    2007-08-01 15:44  Douglas Bates <bates@stat.wisc.edu>
188    
189            * [r4686] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
190              src/chm_common.c, src/chm_common.h: Change API for
191              numeric_as_chm_dense and N_AS_CHM_DN
192    
193    2007-08-01  Martin Maechler  <maechler@stat.math.ethz.ch>
194    
195            * src/dtrMatrix.c (dtrMatrix_matrix_mm): fix dimensionality check (!)
196            * tests/matprod.R: regr.test for it
197    
198    2007-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
199    
200            * R/dMatrix.R: fix from Brian for   Math2(., digits = "missing")
201            * tests/group-methods.R: and regression-test it
202    
203    2007-07-19 19:45  Douglas Bates <bates@stat.wisc.edu>
204    
205            * [r4642] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
206              inst/include/cholmod.h, src/chm_common.c, src/init.c: Export
207              triplet_to_sparse, documentation, use typedefs
208    
209    2007-07-18  Martin Maechler  <maechler@stat.math.ethz.ch>
210    
211            * man/dpoMatrix-class.Rd: added 'corMatrix' example
212    
213            * src/dsyMatrix.[ch] (dsyMatrix_as_matrix): new 'keep_dimnames' arg
214            * src/dtrMatrix.[ch] (dtrMatrix_as_matrix): ditto
215            * src/init.c, R/dsyMatrix.R, R/dtrMatrix.R, R/lgTMatrix.R: ditto
216    
217            * R/lsparseMatrix.R: bug fix in "all" method
218            * R/Ops.R (.do.Logic.lsparse): "|" bug in borderline case
219    
220            * R/dsyMatrix.R (coerce->dsTMatrix): (i,j) slots should *not* have names
221            * R/ngTMatrix.R (coerce->ngTMatrix): ditto;
222                    + matrix |-> nMatrix coercion
223            * R/pMatrix.R: + setAs()  to dMatrix and from nMatrix
224            * man/pMatrix-class.Rd: ditto
225    
226            * R/Matrix.R (Summary): method for non-dMatrix
227    
228            * tests/Class+Meth.R (extraValid): new check about "dirty" slots
229            * tests/Class+Meth.R (tstMatrixClass): test norm(.);
230                    test all Summary methods.
231    
232    2007-07-16  Martin Maechler  <maechler@stat.math.ethz.ch>
233    
234            * R/dgeMatrix.R (norm, rcond): methods for 'matrix'
235    
236    2007-07-14  Martin Maechler  <maechler@stat.math.ethz.ch>
237    
238            * R/sparseMatrix.R (norm): simple methods for sparseMatrix
239    
240            * R/pMatrix.R (t?crossprod): methods for pMatrix
241    
242    2007-07-10  Douglas Bates  <bates@stat.wisc.edu>
243    
244            * src/dgeMatrix.c (dgeMatrix_colsums): Get the logic straight.
245    
246    2007-07-09 20:45  Douglas Bates <bates@stat.wisc.edu>
247    
248            * [r4579] src/dgeMatrix.c: Untangle horrible code in dgeMatrix_colsums
249              trying to fix a subtle bug - which has been somewhere else.
250    
251    2007-07-09 19:43  Martin Maechler <maechler@stat.math.ethz.ch>
252    
253            * [r4578] src/dgeMatrix.c: "cleaned" dgeMatrix_colsums() - but did not
254              solve the bug
255    
256    2007-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
257    
258            * src/dgCMatrix.c (compressed_to_TMatrix):
259    
260    2007-07-07  Martin Maechler  <maechler@stat.math.ethz.ch>
261    
262            * src/Csparse.c (Rsparse_validate): new, to have some validity
263            checking for RsparseMatrix
264            * src/dgCMatrix.c (xRMatrix_validate): ditto
265            * src/dtCMatrix.c (tRMatrix_validate): ditto
266    
267    2007-07-07  Douglas Bates <bates@stat.wisc.edu>
268    
269            * [r4567] R/AllClass.R: Slots already in RsparseMatrix were redefined in
270              lgRMatrix
271            * [r4568] DESCRIPTION: Prepare for bug-fix release
272            * [r4570] src/CHOLMOD/Check/cholmod_write.c: Include cholmod_matrixops.h
273              for declaration of cholmod_symmetry
274    
275    2007-07-06  Martin Maechler  <maechler@stat.math.ethz.ch>
276    
277            * DESCRIPTION (Version): 0.999375 merged into the trunk; ready for
278            release.
279    
280    2007-07-06 14:11  Douglas Bates <bates@stat.wisc.edu>
281    
282            * [r4559] src/iohb.c, src/iohb.h: Remove Harwell-Boeing input/output
283              functions - no longer used
284            * [r4560] src/HBMM.c, src/Mutils.c, src/dgTMatrix.c, src/dgeMatrix.c,
285              src/dspMatrix.c, src/dsyMatrix.c, src/dtCMatrix.c,
286              src/factorizations.c, src/sparseQR.c: Replace most calls to Calloc by
287              Alloca
288    
289    2007-07-06 13:14  Martin Maechler <maechler@stat.math.ethz.ch>
290    
291            * [r4558] inst/doc/Comparisons.Rnw, src/CHMfactor.c, src/Csparse.c,
292              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dense.c,
293              src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c, src/sparseQR.c,
294              src/t_gCMatrix_colSums.c: more R_CheckStack()s
295    
296    2007-07-05 18:12  Douglas Bates <bates@stat.wisc.edu>
297    
298            * [r4550] inst/include/Matrix.h: Add the macro N_AS_CHM_DN to "alloca"
299              the required amount of memory then call M_numeric_as_chm_dense.
300            * [r4556] src/Mutils.h, src/dgCMatrix.c: Define and use the Alloca macro
301              (like Calloc but calling alloca)
302    
303    2007-07-05  Martin Maechler  <maechler@stat.math.ethz.ch>
304    
305            * R/sparseMatrix.R (printSpMatrix): renamed from prSpMatrix()
306            and extended with more sophisticated 'col.names' option.
307            * NAMESPACE: export  printSparseMatrix()
308            * man/printSpMatrix.Rd: document, incl. examples
309    
310    2007-07-04 16:21  Douglas Bates <bates@stat.wisc.edu>
311    
312            * [r4543] src/cs_utils.c, src/cs_utils.h, src/dgCMatrix.c,
313              src/dtCMatrix.c, src/sparseQR.c: CSP typedef for *cs and macro
314              AS_CSP. API change - pass the empty structure to Matrix_as_cs.
315    
316    2007-07-04  Martin Maechler  <maechler@stat.math.ethz.ch>
317    
318            * DESCRIPTION (Version): 0.99875-4
319    
320            * tests/Class+Meth.R (tstMatrixClass): add dimnames, and hence test
321            some dimnames perservation.
322    
323            * R/dsTMatrix.R (t-method): keep dimnames
324            * R/dtTMatrix.R:  ditto
325    
326            * R/sparseMatrix.R (prSpMatrix): print colnames when non-trivial
327            and ncol(.) < 10
328    
329            * src/cs_utils.c: drop check_class() and use Matrix_check_class()
330            from Mutils.h
331    
332            * src/lgCMatrix.c ([ln]csc_to_matrix): no longer lose dimnames,
333            e.g. in as(<ngCMatrix>, "matrix")
334    
335    2007-07-01 13:27  Douglas Bates <bates@stat.wisc.edu>
336    
337            * [r4529] .: Create a branch for the API changes from the 0.99875
338              series to the 0.999375 series
339            * [r4530] DESCRIPTION, inst/include/Matrix.h,
340              inst/include/Matrix_stubs.c, src/CHMfactor.c, src/Csparse.c,
341              src/Mutils.h, src/Tsparse.c, src/chm_common.c, src/chm_common.h,
342              src/dense.c, src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c,
343              src/t_gCMatrix_colSums.c: API change - pass the empty structure to the
344              as_cholmod_x functions
345    
346    2007-06-30 09:05  Martin Maechler <maechler@stat.math.ethz.ch>
347    
348            * [r4527] trunk/Matrix/DESCRIPTION, trunk/Matrix/NAMESPACE,
349              trunk/Matrix/inst/doc/Comparisons.Rnw: add session- and hardware-info
350              to Comparisons
351    
352    >>>>>>> .merge-right.r4561
353    2007-06-29  Martin Maechler  <maechler@stat.math.ethz.ch>
354    
355            * DESCRIPTION (Version): 0.99875-3 ready to be released.
356    
357            * R/sparseMatrix.R (spMatrix): make spMatrix(3,4) working
358    
359            * R/AllGeneric.R: set "Math" (and "Math2") group generics in a way
360            that should also work in a future version of R.
361    
362    2007-06-21  Martin Maechler  <maechler@stat.math.ethz.ch>
363    
364            * NAMESPACE, R/AllClass.R: "xsparseVector" class union.
365    
366            * R/sparseVector.R: more *sparseVector coercions, notably for
367            non - double ones.
368    
369    2007-06-19  Martin Maechler  <maechler@stat.math.ethz.ch>
370    
371            * R/colSums.R: new file for all (col|row)(Sums|Means) methods,
372              notably the new ones building on the new .Call(.)s:
373    
374            * src/dgCMatrix.c (DEF_gCMatrix_COLSUMS): use to define
375            all 4 of [dlin]gCMatrix_colSums().
376    
377    2007-06-18 16:12  Douglas Bates <bates@stat.wisc.edu>
378    
379            * [r4472] src/Syms.h, src/init.c: Added Matrix_lengthSym
380            * [r4473] src/dgCMatrix.c: Modified dgCMatrix_colSums for sparseVector
381              result
382    
383  2007-06-16  Martin Maechler  <maechler@stat.math.ethz.ch>  2007-06-16  Martin Maechler  <maechler@stat.math.ethz.ch>
384    
385            * R/kronecker.R: fix typo (could lead to inf.recursion)
386            * test/simple.R: testing that
387    
388          * R/sparseMatrix.R (prSpMatrix): change to be used as print()          * R/sparseMatrix.R (prSpMatrix): change to be used as print()
389          method (which can have arguments, show() can't).          method as well (which can have arguments, show() can't).
390    
391  2007-06-16 15:52  Douglas Bates <bates@stat.wisc.edu>  2007-06-16 15:52  Douglas Bates <bates@stat.wisc.edu>
392    

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