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revision 1922, Sat Jun 23 18:08:48 2007 UTC revision 2108, Fri Jan 25 11:14:32 2008 UTC
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1    2008-01-24  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * R/Ops.R (.Arith.Csparse): new utility factored out of former
4              <dgC> o <dgC>, extended for triangular and also used in  <dtC> o <dtC>.
5    
6    2008-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
7    
8            * tests/factorizing.R (checkSchur): and more tests for checking Schur()
9    
10            * inst/test-tools.R (isOrthogonal): new function; also file restructured
11    
12    2008-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
13    
14            * R/ngTMatrix.R: allow as(<numeric matrix>, "ngTMatrix") and hence
15            coercion to "nMatrix" and "pMatrix"
16    
17            * R/AllClass.R: "Schur" class;  "number" class union
18            * man/number-class.Rd:
19            * man/Schur-class.Rd:
20    
21            * R/eigen.R (.dgeSchur): utility, and return "Schur" class
22            (.simpleSchur): Schur() method for diagonal matrices
23            (.triSchur):    Schur() method for triangular matrices
24            (Schur.sym):    Schur() for symmetric matrices {building on eigen()}.
25    
26    
27    2008-01-21  Martin Maechler  <maechler@stat.math.ethz.ch>
28    
29            * src/dgCMatrix.c (dgCMatrix_QR): set @Dim slot (as per doc)
30    
31    2008-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
32    
33            * R/CHMfactor.R (solve): method for b="numeric", but also b="ANY"
34                    in order to ensure 'system = *' is not lost;
35                    formals()$system instead of cut&paste.
36            * tests/factorizing.R: test solve(<CHM..>, <numeric>)
37    
38    2008-01-11  Martin Maechler  <maechler@stat.math.ethz.ch>
39    
40            * DESCRIPTION (Date): make ready for release --> 0.999375-4
41    
42            * R/dgeMatrix.R: fix rcond() method for "dgeMatrix".
43    
44    2007-12-08  Martin Maechler  <maechler@stat.math.ethz.ch>
45    
46            * R/pMatrix.R: as(*, "matrix") now returns 0/1 *integer* matrix,
47                    and hence does as.vector(.).
48            * man/pMatrix-class.Rd: docs
49            * R/sparseMatrix.R: fix for printing "integer sparse"
50    
51            * tests/Class+Meth.R (tstMatrixClass): test M[FALSE], M[2] etc
52    
53            * R/Matrix.R and others: use "exact" function argument list for
54                    both "["   : (x, i,j, ..., drop)
55                    and  "[<-" : (x, i,j, ..., value)
56    
57            * R/denseMatrix.R: M[i] and M[i] <- v  (i vector) now work
58            * R/Tsparse.R (replTmat):    ditto
59            * R/diagMatrix.R (replDiag): ditto
60            * R/Csparse.R (replCmat):    ditto {was it worth the pain?}
61            * tests/indexing.R: testing the above
62    
63    2007-12-07  Martin Maechler  <maechler@stat.math.ethz.ch>
64    
65            * R/sparseMatrix.R (cov2cor): method for sparse matrices
66    
67            * R/diagMatrix.R ([<-): fix   D[ cbind(i,j) ] <- v
68    
69            * R/bind2.R: fix for Rsparse* and rbind2(dense,dense)
70    
71            * tests/Class+Meth.R: test cbind2, rbind2  and  diag<-
72    
73    2007-12-06  Martin Maechler  <maechler@stat.math.ethz.ch>
74    
75            * R/Matrix.R: "generic" cov2cor() method
76    
77            * R/nearPD.R: new 'only.values', 'keepDiag' arguments;
78                    speed up Q %*% D %*% t(Q)
79            * tests/dpoMatrix.R: test nearPD()
80    
81    2007-12-05  Doug Bates and Martin Maechler
82    
83            * R/sparseMatrix.R: xtabs(*, sparse=.) function; an extention of
84            stats::xtabs() allowing to create sparse matrices.
85    
86    2007-10-08  Martin Maechler  <maechler@stat.math.ethz.ch>
87    
88            * DESCRIPTION (Version): *-4 (released *-3 two days ago)
89    
90    2007-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
91    
92            * R/pMatrix.R: solve(<Matrix>, <pMatrix>)
93    
94    2007-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
95    
96            * R/LU.R: solve() method for "denseLU"
97    
98    2007-10-01  Martin Maechler  <maechler@stat.math.ethz.ch>
99    
100            * DESCRIPTION (Version): 0.999375-3 preparing for release
101    
102            * R/AllGeneric.R: simplify  if(.) .. else .. for R <= 2.5.1
103    
104            * R/Matrix.R (Matrix): .Internal(matrix(..)) different for R >= 2.7.0
105    
106    2007-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
107    
108            * R/pMatrix.R (.m.mult.pMat): fix <matrix> %*% <pMatrix>,
109              thanks to Kasper Kristensen.
110            * tests/matprod.R: regression test for that.
111    
112    2007-09-23 17:32  Douglas Bates <bates@stat.wisc.edu>
113    
114            * [r4778] R/AllGeneric.R: Check R version before defining generics for
115              primitives
116    
117    2007-09-13  Martin Maechler  <maechler@stat.math.ethz.ch>
118    
119            * R/denseMatrix.R (rcond): method
120            * R/sparseQR.R (rcond): method, use x or t(x)
121    
122    2007-09-12  Martin Maechler  <maechler@stat.math.ethz.ch>
123    
124            * R/dgeMatrix.R (rcond): method: work via qr.R() for non-square
125            matrices.
126            * R/sparseMatrix.R: Ditto for all other rcond() method definitions.
127    
128            * man/rcond.Rd: mention the more general definition, and add
129            example for non-square matrices.
130    
131            * man/chol.Rd: new file, for the S4 chol() generic and all methods.
132    
133    2007-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
134    
135            * R/sparseQR.R: add qr.R() method [to be used for rcond()]
136    
137    2007-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
138    
139            * R/Matrix.R ([<-): add (Matrix,missing,ANY,Matrix) etc
140            * tests/indexing.R: add new regression for the above cases.
141    
142    2007-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
143    
144            * src/Mutils.h (__sun): clause for alloca.h on Solaris
145    
146    2007-08-16  Martin Maechler  <maechler@stat.math.ethz.ch>
147    
148            * DESCRIPTION (Date, Version): 0.999375-2
149    
150    2007-08-15  Martin Maechler  <maechler@stat.math.ethz.ch>
151    
152            * R/HBMM.R (readMM): make work for pattern matrices as well
153    
154    2007-08-14 13:07  Douglas Bates <bates@stat.wisc.edu>
155    
156            * [r4730] src/Mutils.h: declare alloca
157            * [r4734] NAMESPACE, R/AllGeneric.R, R/Csparse.R, R/HBMM.R, R/Tsparse.R,
158              R/dgCMatrix.R, R/dgTMatrix.R, R/dsCMatrix.R, R/dsTMatrix.R,
159              man/externalFormats.Rd, src/Csparse.c, src/Csparse.h, src/DEPS.mkf,
160              src/HBMM.c, src/HBMM.h, src/Mutils.h, src/SOURCES_C.mkf, src/init.c,
161              src/mmio.c, src/mmio.h: Remove deprecated function writeHB and its
162              methods; switch writeMM to use CHOLMOD code; repair readMM
163    
164    2007-08-14  Martin Maechler  <maechler@stat.math.ethz.ch>
165    
166            * R/nearPD.R, man/nearPD.Rd (nearPD): new function built on Jens
167            Oehlschlaegel's ... result type still to be discussed!
168    
169    2007-08-10  Martin Maechler  <maechler@stat.math.ethz.ch>
170    
171            * man/image-methods.Rd: new, combining all image() methods
172    
173    2007-08-09  Martin Maechler  <maechler@stat.math.ethz.ch>
174    
175            * R/dgCMatrix.R: define qr() and lu() methods for "sparseMatrix"
176            to work via dgC...
177    
178            * R/Matrix.R (Matrix): special treatment for "table" (S3)
179    
180    2007-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
181    
182            * R/dgTMatrix.R (image): change defaults to
183                    aspect = "iso", colorkey = FALSE
184    
185    2007-08-06  Martin Maechler  <maechler@stat.math.ethz.ch>
186    
187            * src/dsyMatrix.c (dsyMatrix_matrix_mm): 'b' might be matrix;
188            must copy its *expanded* x slot before LAPACK call.
189    
190            * tests/matprod.R: test the last days' changes.
191    
192    2007-08-06 16:43  Douglas Bates <bates@stat.wisc.edu>
193    
194            * [r4712] inst/include/Matrix_stubs.c: Change R_cholmod_printf in stubs
195              as well as in sources
196            * [r4713] src/dsyMatrix.c: Duplicate the contents of the RHS before
197              Lapack call
198    
199    2007-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
200    
201            * R/Matrix.R (%*%, crossprod, tcrossprod): add method for
202                    ("Matrix", "matrix") which is needed in some cases.
203            Ditto for solve().
204    
205            * R/colSums.R (.as.dge.Fun): need ddenseMatrix methods to avoid
206            infinite recursion in dispatch for some cases.
207    
208    2007-08-02 08:48  Martin Maechler <maechler@stat.math.ethz.ch>
209    
210            * [r4693] src/chm_common.c: R_cholmod_printf() instead of Rprintf() just
211              so pointers match
212    
213    2007-08-02  Martin Maechler  <maechler@stat.math.ethz.ch>
214    
215            * DESCRIPTION (Date): set ready for release -- 0.999375-1
216    
217    2007-08-01 15:44  Douglas Bates <bates@stat.wisc.edu>
218    
219            * [r4686] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
220              src/chm_common.c, src/chm_common.h: Change API for
221              numeric_as_chm_dense and N_AS_CHM_DN
222    
223    2007-08-01  Martin Maechler  <maechler@stat.math.ethz.ch>
224    
225            * src/dtrMatrix.c (dtrMatrix_matrix_mm): fix dimensionality check (!)
226            * tests/matprod.R: regr.test for it
227    
228    2007-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
229    
230            * R/dMatrix.R: fix from Brian for   Math2(., digits = "missing")
231            * tests/group-methods.R: and regression-test it
232    
233    2007-07-19 19:45  Douglas Bates <bates@stat.wisc.edu>
234    
235            * [r4642] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
236              inst/include/cholmod.h, src/chm_common.c, src/init.c: Export
237              triplet_to_sparse, documentation, use typedefs
238    
239    2007-07-18  Martin Maechler  <maechler@stat.math.ethz.ch>
240    
241            * man/dpoMatrix-class.Rd: added 'corMatrix' example
242    
243            * src/dsyMatrix.[ch] (dsyMatrix_as_matrix): new 'keep_dimnames' arg
244            * src/dtrMatrix.[ch] (dtrMatrix_as_matrix): ditto
245            * src/init.c, R/dsyMatrix.R, R/dtrMatrix.R, R/lgTMatrix.R: ditto
246    
247            * R/lsparseMatrix.R: bug fix in "all" method
248            * R/Ops.R (.do.Logic.lsparse): "|" bug in borderline case
249    
250            * R/dsyMatrix.R (coerce->dsTMatrix): (i,j) slots should *not* have names
251            * R/ngTMatrix.R (coerce->ngTMatrix): ditto;
252                    + matrix |-> nMatrix coercion
253            * R/pMatrix.R: + setAs()  to dMatrix and from nMatrix
254            * man/pMatrix-class.Rd: ditto
255    
256            * R/Matrix.R (Summary): method for non-dMatrix
257    
258            * tests/Class+Meth.R (extraValid): new check about "dirty" slots
259            * tests/Class+Meth.R (tstMatrixClass): test norm(.);
260                    test all Summary methods.
261    
262    2007-07-16  Martin Maechler  <maechler@stat.math.ethz.ch>
263    
264            * R/dgeMatrix.R (norm, rcond): methods for 'matrix'
265    
266    2007-07-14  Martin Maechler  <maechler@stat.math.ethz.ch>
267    
268            * R/sparseMatrix.R (norm): simple methods for sparseMatrix
269    
270            * R/pMatrix.R (t?crossprod): methods for pMatrix
271    
272    2007-07-10  Douglas Bates  <bates@stat.wisc.edu>
273    
274            * src/dgeMatrix.c (dgeMatrix_colsums): Get the logic straight.
275    
276    2007-07-09 20:45  Douglas Bates <bates@stat.wisc.edu>
277    
278            * [r4579] src/dgeMatrix.c: Untangle horrible code in dgeMatrix_colsums
279              trying to fix a subtle bug - which has been somewhere else.
280    
281    2007-07-09 19:43  Martin Maechler <maechler@stat.math.ethz.ch>
282    
283            * [r4578] src/dgeMatrix.c: "cleaned" dgeMatrix_colsums() - but did not
284              solve the bug
285    
286    2007-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
287    
288            * src/dgCMatrix.c (compressed_to_TMatrix):
289    
290    2007-07-07  Martin Maechler  <maechler@stat.math.ethz.ch>
291    
292            * src/Csparse.c (Rsparse_validate): new, to have some validity
293            checking for RsparseMatrix
294            * src/dgCMatrix.c (xRMatrix_validate): ditto
295            * src/dtCMatrix.c (tRMatrix_validate): ditto
296    
297    2007-07-07  Douglas Bates <bates@stat.wisc.edu>
298    
299            * [r4567] R/AllClass.R: Slots already in RsparseMatrix were redefined in
300              lgRMatrix
301            * [r4568] DESCRIPTION: Prepare for bug-fix release
302            * [r4570] src/CHOLMOD/Check/cholmod_write.c: Include cholmod_matrixops.h
303              for declaration of cholmod_symmetry
304    
305    2007-07-06  Martin Maechler  <maechler@stat.math.ethz.ch>
306    
307            * DESCRIPTION (Version): 0.999375 merged into the trunk; ready for
308            release.
309    
310    2007-07-06 14:11  Douglas Bates <bates@stat.wisc.edu>
311    
312            * [r4559] src/iohb.c, src/iohb.h: Remove Harwell-Boeing input/output
313              functions - no longer used
314            * [r4560] src/HBMM.c, src/Mutils.c, src/dgTMatrix.c, src/dgeMatrix.c,
315              src/dspMatrix.c, src/dsyMatrix.c, src/dtCMatrix.c,
316              src/factorizations.c, src/sparseQR.c: Replace most calls to Calloc by
317              Alloca
318    
319    2007-07-06 13:14  Martin Maechler <maechler@stat.math.ethz.ch>
320    
321            * [r4558] inst/doc/Comparisons.Rnw, src/CHMfactor.c, src/Csparse.c,
322              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dense.c,
323              src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c, src/sparseQR.c,
324              src/t_gCMatrix_colSums.c: more R_CheckStack()s
325    
326    2007-07-05 18:12  Douglas Bates <bates@stat.wisc.edu>
327    
328            * [r4550] inst/include/Matrix.h: Add the macro N_AS_CHM_DN to "alloca"
329              the required amount of memory then call M_numeric_as_chm_dense.
330            * [r4556] src/Mutils.h, src/dgCMatrix.c: Define and use the Alloca macro
331              (like Calloc but calling alloca)
332    
333    2007-07-05  Martin Maechler  <maechler@stat.math.ethz.ch>
334    
335            * R/sparseMatrix.R (printSpMatrix): renamed from prSpMatrix()
336            and extended with more sophisticated 'col.names' option.
337            * NAMESPACE: export  printSparseMatrix()
338            * man/printSpMatrix.Rd: document, incl. examples
339    
340    2007-07-04 16:21  Douglas Bates <bates@stat.wisc.edu>
341    
342            * [r4543] src/cs_utils.c, src/cs_utils.h, src/dgCMatrix.c,
343              src/dtCMatrix.c, src/sparseQR.c: CSP typedef for *cs and macro
344              AS_CSP. API change - pass the empty structure to Matrix_as_cs.
345    
346    2007-07-04  Martin Maechler  <maechler@stat.math.ethz.ch>
347    
348            * DESCRIPTION (Version): 0.99875-4
349    
350            * tests/Class+Meth.R (tstMatrixClass): add dimnames, and hence test
351            some dimnames perservation.
352    
353            * R/dsTMatrix.R (t-method): keep dimnames
354            * R/dtTMatrix.R:  ditto
355    
356            * R/sparseMatrix.R (prSpMatrix): print colnames when non-trivial
357            and ncol(.) < 10
358    
359            * src/cs_utils.c: drop check_class() and use Matrix_check_class()
360            from Mutils.h
361    
362            * src/lgCMatrix.c ([ln]csc_to_matrix): no longer lose dimnames,
363            e.g. in as(<ngCMatrix>, "matrix")
364    
365    2007-07-01 13:27  Douglas Bates <bates@stat.wisc.edu>
366    
367            * [r4529] .: Create a branch for the API changes from the 0.99875
368              series to the 0.999375 series
369            * [r4530] DESCRIPTION, inst/include/Matrix.h,
370              inst/include/Matrix_stubs.c, src/CHMfactor.c, src/Csparse.c,
371              src/Mutils.h, src/Tsparse.c, src/chm_common.c, src/chm_common.h,
372              src/dense.c, src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c,
373              src/t_gCMatrix_colSums.c: API change - pass the empty structure to the
374              as_cholmod_x functions
375    
376    2007-06-30 09:05  Martin Maechler <maechler@stat.math.ethz.ch>
377    
378            * [r4527] trunk/Matrix/DESCRIPTION, trunk/Matrix/NAMESPACE,
379              trunk/Matrix/inst/doc/Comparisons.Rnw: add session- and hardware-info
380              to Comparisons
381    
382    >>>>>>> .merge-right.r4561
383    2007-06-29  Martin Maechler  <maechler@stat.math.ethz.ch>
384    
385            * DESCRIPTION (Version): 0.99875-3 ready to be released.
386    
387            * R/sparseMatrix.R (spMatrix): make spMatrix(3,4) working
388    
389            * R/AllGeneric.R: set "Math" (and "Math2") group generics in a way
390            that should also work in a future version of R.
391    
392  2007-06-21  Martin Maechler  <maechler@stat.math.ethz.ch>  2007-06-21  Martin Maechler  <maechler@stat.math.ethz.ch>
393    
394          * NAMESPACE, R/AllClass.R: "xsparseVector" class union.          * NAMESPACE, R/AllClass.R: "xsparseVector" class union.
# Line 5  Line 396 
396          * R/sparseVector.R: more *sparseVector coercions, notably for          * R/sparseVector.R: more *sparseVector coercions, notably for
397          non - double ones.          non - double ones.
398    
   
399  2007-06-19  Martin Maechler  <maechler@stat.math.ethz.ch>  2007-06-19  Martin Maechler  <maechler@stat.math.ethz.ch>
400    
401          * R/colSums.R: new file for all (col|row)(Sums|Means) methods,          * R/colSums.R: new file for all (col|row)(Sums|Means) methods,

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