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revision 1922, Sat Jun 23 18:08:48 2007 UTC revision 2102, Fri Jan 11 22:35:25 2008 UTC
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1    2008-01-11  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * DESCRIPTION (Date): make ready for release
4    
5            * R/dgeMatrix.R: fix rcond() method for "dgeMatrix".
6    
7    2007-12-08  Martin Maechler  <maechler@stat.math.ethz.ch>
8    
9            * R/pMatrix.R: as(*, "matrix") now returns 0/1 *integer* matrix,
10                    and hence does as.vector(.).
11            * man/pMatrix-class.Rd: docs
12            * R/sparseMatrix.R: fix for printing "integer sparse"
13    
14            * tests/Class+Meth.R (tstMatrixClass): test M[FALSE], M[2] etc
15    
16            * R/Matrix.R and others: use "exact" function argument list for
17                    both "["   : (x, i,j, ..., drop)
18                    and  "[<-" : (x, i,j, ..., value)
19    
20            * R/denseMatrix.R: M[i] and M[i] <- v  (i vector) now work
21            * R/Tsparse.R (replTmat):    ditto
22            * R/diagMatrix.R (replDiag): ditto
23            * R/Csparse.R (replCmat):    ditto {was it worth the pain?}
24            * tests/indexing.R: testing the above
25    
26    2007-12-07  Martin Maechler  <maechler@stat.math.ethz.ch>
27    
28            * R/sparseMatrix.R (cov2cor): method for sparse matrices
29    
30            * R/diagMatrix.R ([<-): fix   D[ cbind(i,j) ] <- v
31    
32            * R/bind2.R: fix for Rsparse* and rbind2(dense,dense)
33    
34            * tests/Class+Meth.R: test cbind2, rbind2  and  diag<-
35    
36    2007-12-06  Martin Maechler  <maechler@stat.math.ethz.ch>
37    
38            * R/Matrix.R: "generic" cov2cor() method
39    
40            * R/nearPD.R: new 'only.values', 'keepDiag' arguments;
41                    speed up Q %*% D %*% t(Q)
42            * tests/dpoMatrix.R: test nearPD()
43    
44    2007-12-05  Doug Bates and Martin Maechler
45    
46            * R/sparseMatrix.R: xtabs(*, sparse=.) function; an extention of
47            stats::xtabs() allowing to create sparse matrices.
48    
49    2007-10-08  Martin Maechler  <maechler@stat.math.ethz.ch>
50    
51            * DESCRIPTION (Version): *-4 (released *-3 two days ago)
52    
53    2007-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
54    
55            * R/pMatrix.R: solve(<Matrix>, <pMatrix>)
56    
57    2007-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
58    
59            * R/LU.R: solve() method for "denseLU"
60    
61    2007-10-01  Martin Maechler  <maechler@stat.math.ethz.ch>
62    
63            * DESCRIPTION (Version): 0.999375-3 preparing for release
64    
65            * R/AllGeneric.R: simplify  if(.) .. else .. for R <= 2.5.1
66    
67            * R/Matrix.R (Matrix): .Internal(matrix(..)) different for R >= 2.7.0
68    
69    2007-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
70    
71            * R/pMatrix.R (.m.mult.pMat): fix <matrix> %*% <pMatrix>,
72              thanks to Kasper Kristensen.
73            * tests/matprod.R: regression test for that.
74    
75    2007-09-23 17:32  Douglas Bates <bates@stat.wisc.edu>
76    
77            * [r4778] R/AllGeneric.R: Check R version before defining generics for
78              primitives
79    
80    2007-09-13  Martin Maechler  <maechler@stat.math.ethz.ch>
81    
82            * R/denseMatrix.R (rcond): method
83            * R/sparseQR.R (rcond): method, use x or t(x)
84    
85    2007-09-12  Martin Maechler  <maechler@stat.math.ethz.ch>
86    
87            * R/dgeMatrix.R (rcond): method: work via qr.R() for non-square
88            matrices.
89            * R/sparseMatrix.R: Ditto for all other rcond() method definitions.
90    
91            * man/rcond.Rd: mention the more general definition, and add
92            example for non-square matrices.
93    
94            * man/chol.Rd: new file, for the S4 chol() generic and all methods.
95    
96    2007-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
97    
98            * R/sparseQR.R: add qr.R() method [to be used for rcond()]
99    
100    2007-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
101    
102            * R/Matrix.R ([<-): add (Matrix,missing,ANY,Matrix) etc
103            * tests/indexing.R: add new regression for the above cases.
104    
105    2007-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
106    
107            * src/Mutils.h (__sun): clause for alloca.h on Solaris
108    
109    2007-08-16  Martin Maechler  <maechler@stat.math.ethz.ch>
110    
111            * DESCRIPTION (Date, Version): 0.999375-2
112    
113    2007-08-15  Martin Maechler  <maechler@stat.math.ethz.ch>
114    
115            * R/HBMM.R (readMM): make work for pattern matrices as well
116    
117    2007-08-14 13:07  Douglas Bates <bates@stat.wisc.edu>
118    
119            * [r4730] src/Mutils.h: declare alloca
120            * [r4734] NAMESPACE, R/AllGeneric.R, R/Csparse.R, R/HBMM.R, R/Tsparse.R,
121              R/dgCMatrix.R, R/dgTMatrix.R, R/dsCMatrix.R, R/dsTMatrix.R,
122              man/externalFormats.Rd, src/Csparse.c, src/Csparse.h, src/DEPS.mkf,
123              src/HBMM.c, src/HBMM.h, src/Mutils.h, src/SOURCES_C.mkf, src/init.c,
124              src/mmio.c, src/mmio.h: Remove deprecated function writeHB and its
125              methods; switch writeMM to use CHOLMOD code; repair readMM
126    
127    2007-08-14  Martin Maechler  <maechler@stat.math.ethz.ch>
128    
129            * R/nearPD.R, man/nearPD.Rd (nearPD): new function built on Jens
130            Oehlschlaegel's ... result type still to be discussed!
131    
132    2007-08-10  Martin Maechler  <maechler@stat.math.ethz.ch>
133    
134            * man/image-methods.Rd: new, combining all image() methods
135    
136    2007-08-09  Martin Maechler  <maechler@stat.math.ethz.ch>
137    
138            * R/dgCMatrix.R: define qr() and lu() methods for "sparseMatrix"
139            to work via dgC...
140    
141            * R/Matrix.R (Matrix): special treatment for "table" (S3)
142    
143    2007-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
144    
145            * R/dgTMatrix.R (image): change defaults to
146                    aspect = "iso", colorkey = FALSE
147    
148    2007-08-06  Martin Maechler  <maechler@stat.math.ethz.ch>
149    
150            * src/dsyMatrix.c (dsyMatrix_matrix_mm): 'b' might be matrix;
151            must copy its *expanded* x slot before LAPACK call.
152    
153            * tests/matprod.R: test the last days' changes.
154    
155    2007-08-06 16:43  Douglas Bates <bates@stat.wisc.edu>
156    
157            * [r4712] inst/include/Matrix_stubs.c: Change R_cholmod_printf in stubs
158              as well as in sources
159            * [r4713] src/dsyMatrix.c: Duplicate the contents of the RHS before
160              Lapack call
161    
162    2007-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
163    
164            * R/Matrix.R (%*%, crossprod, tcrossprod): add method for
165                    ("Matrix", "matrix") which is needed in some cases.
166            Ditto for solve().
167    
168            * R/colSums.R (.as.dge.Fun): need ddenseMatrix methods to avoid
169            infinite recursion in dispatch for some cases.
170    
171    2007-08-02 08:48  Martin Maechler <maechler@stat.math.ethz.ch>
172    
173            * [r4693] src/chm_common.c: R_cholmod_printf() instead of Rprintf() just
174              so pointers match
175    
176    2007-08-02  Martin Maechler  <maechler@stat.math.ethz.ch>
177    
178            * DESCRIPTION (Date): set ready for release -- 0.999375-1
179    
180    2007-08-01 15:44  Douglas Bates <bates@stat.wisc.edu>
181    
182            * [r4686] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
183              src/chm_common.c, src/chm_common.h: Change API for
184              numeric_as_chm_dense and N_AS_CHM_DN
185    
186    2007-08-01  Martin Maechler  <maechler@stat.math.ethz.ch>
187    
188            * src/dtrMatrix.c (dtrMatrix_matrix_mm): fix dimensionality check (!)
189            * tests/matprod.R: regr.test for it
190    
191    2007-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
192    
193            * R/dMatrix.R: fix from Brian for   Math2(., digits = "missing")
194            * tests/group-methods.R: and regression-test it
195    
196    2007-07-19 19:45  Douglas Bates <bates@stat.wisc.edu>
197    
198            * [r4642] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
199              inst/include/cholmod.h, src/chm_common.c, src/init.c: Export
200              triplet_to_sparse, documentation, use typedefs
201    
202    2007-07-18  Martin Maechler  <maechler@stat.math.ethz.ch>
203    
204            * man/dpoMatrix-class.Rd: added 'corMatrix' example
205    
206            * src/dsyMatrix.[ch] (dsyMatrix_as_matrix): new 'keep_dimnames' arg
207            * src/dtrMatrix.[ch] (dtrMatrix_as_matrix): ditto
208            * src/init.c, R/dsyMatrix.R, R/dtrMatrix.R, R/lgTMatrix.R: ditto
209    
210            * R/lsparseMatrix.R: bug fix in "all" method
211            * R/Ops.R (.do.Logic.lsparse): "|" bug in borderline case
212    
213            * R/dsyMatrix.R (coerce->dsTMatrix): (i,j) slots should *not* have names
214            * R/ngTMatrix.R (coerce->ngTMatrix): ditto;
215                    + matrix |-> nMatrix coercion
216            * R/pMatrix.R: + setAs()  to dMatrix and from nMatrix
217            * man/pMatrix-class.Rd: ditto
218    
219            * R/Matrix.R (Summary): method for non-dMatrix
220    
221            * tests/Class+Meth.R (extraValid): new check about "dirty" slots
222            * tests/Class+Meth.R (tstMatrixClass): test norm(.);
223                    test all Summary methods.
224    
225    2007-07-16  Martin Maechler  <maechler@stat.math.ethz.ch>
226    
227            * R/dgeMatrix.R (norm, rcond): methods for 'matrix'
228    
229    2007-07-14  Martin Maechler  <maechler@stat.math.ethz.ch>
230    
231            * R/sparseMatrix.R (norm): simple methods for sparseMatrix
232    
233            * R/pMatrix.R (t?crossprod): methods for pMatrix
234    
235    2007-07-10  Douglas Bates  <bates@stat.wisc.edu>
236    
237            * src/dgeMatrix.c (dgeMatrix_colsums): Get the logic straight.
238    
239    2007-07-09 20:45  Douglas Bates <bates@stat.wisc.edu>
240    
241            * [r4579] src/dgeMatrix.c: Untangle horrible code in dgeMatrix_colsums
242              trying to fix a subtle bug - which has been somewhere else.
243    
244    2007-07-09 19:43  Martin Maechler <maechler@stat.math.ethz.ch>
245    
246            * [r4578] src/dgeMatrix.c: "cleaned" dgeMatrix_colsums() - but did not
247              solve the bug
248    
249    2007-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
250    
251            * src/dgCMatrix.c (compressed_to_TMatrix):
252    
253    2007-07-07  Martin Maechler  <maechler@stat.math.ethz.ch>
254    
255            * src/Csparse.c (Rsparse_validate): new, to have some validity
256            checking for RsparseMatrix
257            * src/dgCMatrix.c (xRMatrix_validate): ditto
258            * src/dtCMatrix.c (tRMatrix_validate): ditto
259    
260    2007-07-07  Douglas Bates <bates@stat.wisc.edu>
261    
262            * [r4567] R/AllClass.R: Slots already in RsparseMatrix were redefined in
263              lgRMatrix
264            * [r4568] DESCRIPTION: Prepare for bug-fix release
265            * [r4570] src/CHOLMOD/Check/cholmod_write.c: Include cholmod_matrixops.h
266              for declaration of cholmod_symmetry
267    
268    2007-07-06  Martin Maechler  <maechler@stat.math.ethz.ch>
269    
270            * DESCRIPTION (Version): 0.999375 merged into the trunk; ready for
271            release.
272    
273    2007-07-06 14:11  Douglas Bates <bates@stat.wisc.edu>
274    
275            * [r4559] src/iohb.c, src/iohb.h: Remove Harwell-Boeing input/output
276              functions - no longer used
277            * [r4560] src/HBMM.c, src/Mutils.c, src/dgTMatrix.c, src/dgeMatrix.c,
278              src/dspMatrix.c, src/dsyMatrix.c, src/dtCMatrix.c,
279              src/factorizations.c, src/sparseQR.c: Replace most calls to Calloc by
280              Alloca
281    
282    2007-07-06 13:14  Martin Maechler <maechler@stat.math.ethz.ch>
283    
284            * [r4558] inst/doc/Comparisons.Rnw, src/CHMfactor.c, src/Csparse.c,
285              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dense.c,
286              src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c, src/sparseQR.c,
287              src/t_gCMatrix_colSums.c: more R_CheckStack()s
288    
289    2007-07-05 18:12  Douglas Bates <bates@stat.wisc.edu>
290    
291            * [r4550] inst/include/Matrix.h: Add the macro N_AS_CHM_DN to "alloca"
292              the required amount of memory then call M_numeric_as_chm_dense.
293            * [r4556] src/Mutils.h, src/dgCMatrix.c: Define and use the Alloca macro
294              (like Calloc but calling alloca)
295    
296    2007-07-05  Martin Maechler  <maechler@stat.math.ethz.ch>
297    
298            * R/sparseMatrix.R (printSpMatrix): renamed from prSpMatrix()
299            and extended with more sophisticated 'col.names' option.
300            * NAMESPACE: export  printSparseMatrix()
301            * man/printSpMatrix.Rd: document, incl. examples
302    
303    2007-07-04 16:21  Douglas Bates <bates@stat.wisc.edu>
304    
305            * [r4543] src/cs_utils.c, src/cs_utils.h, src/dgCMatrix.c,
306              src/dtCMatrix.c, src/sparseQR.c: CSP typedef for *cs and macro
307              AS_CSP. API change - pass the empty structure to Matrix_as_cs.
308    
309    2007-07-04  Martin Maechler  <maechler@stat.math.ethz.ch>
310    
311            * DESCRIPTION (Version): 0.99875-4
312    
313            * tests/Class+Meth.R (tstMatrixClass): add dimnames, and hence test
314            some dimnames perservation.
315    
316            * R/dsTMatrix.R (t-method): keep dimnames
317            * R/dtTMatrix.R:  ditto
318    
319            * R/sparseMatrix.R (prSpMatrix): print colnames when non-trivial
320            and ncol(.) < 10
321    
322            * src/cs_utils.c: drop check_class() and use Matrix_check_class()
323            from Mutils.h
324    
325            * src/lgCMatrix.c ([ln]csc_to_matrix): no longer lose dimnames,
326            e.g. in as(<ngCMatrix>, "matrix")
327    
328    2007-07-01 13:27  Douglas Bates <bates@stat.wisc.edu>
329    
330            * [r4529] .: Create a branch for the API changes from the 0.99875
331              series to the 0.999375 series
332            * [r4530] DESCRIPTION, inst/include/Matrix.h,
333              inst/include/Matrix_stubs.c, src/CHMfactor.c, src/Csparse.c,
334              src/Mutils.h, src/Tsparse.c, src/chm_common.c, src/chm_common.h,
335              src/dense.c, src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c,
336              src/t_gCMatrix_colSums.c: API change - pass the empty structure to the
337              as_cholmod_x functions
338    
339    2007-06-30 09:05  Martin Maechler <maechler@stat.math.ethz.ch>
340    
341            * [r4527] trunk/Matrix/DESCRIPTION, trunk/Matrix/NAMESPACE,
342              trunk/Matrix/inst/doc/Comparisons.Rnw: add session- and hardware-info
343              to Comparisons
344    
345    >>>>>>> .merge-right.r4561
346    2007-06-29  Martin Maechler  <maechler@stat.math.ethz.ch>
347    
348            * DESCRIPTION (Version): 0.99875-3 ready to be released.
349    
350            * R/sparseMatrix.R (spMatrix): make spMatrix(3,4) working
351    
352            * R/AllGeneric.R: set "Math" (and "Math2") group generics in a way
353            that should also work in a future version of R.
354    
355  2007-06-21  Martin Maechler  <maechler@stat.math.ethz.ch>  2007-06-21  Martin Maechler  <maechler@stat.math.ethz.ch>
356    
357          * NAMESPACE, R/AllClass.R: "xsparseVector" class union.          * NAMESPACE, R/AllClass.R: "xsparseVector" class union.
# Line 5  Line 359 
359          * R/sparseVector.R: more *sparseVector coercions, notably for          * R/sparseVector.R: more *sparseVector coercions, notably for
360          non - double ones.          non - double ones.
361    
   
362  2007-06-19  Martin Maechler  <maechler@stat.math.ethz.ch>  2007-06-19  Martin Maechler  <maechler@stat.math.ethz.ch>
363    
364          * 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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