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revision 1852, Mon May 21 16:42:35 2007 UTC revision 2081, Sat Oct 6 22:01:45 2007 UTC
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1    2007-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * R/pMatrix.R: solve(<Matrix>, <pMatrix>)
4    
5    2007-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
6    
7            * R/LU.R: solve() method for "denseLU"
8    
9    2007-10-01  Martin Maechler  <maechler@stat.math.ethz.ch>
10    
11            * DESCRIPTION (Version): 0.999375-3 preparing for release
12    
13            * R/AllGeneric.R: simplify  if(.) .. else .. for R <= 2.5.1
14    
15            * R/Matrix.R (Matrix): .Internal(matrix(..)) different for R >= 2.7.0
16    
17    2007-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
18    
19            * R/pMatrix.R (.m.mult.pMat): fix <matrix> %*% <pMatrix>,
20              thanks to Kasper Kristensen.
21            * tests/matprod.R: regression test for that.
22    
23    2007-09-23 17:32  Douglas Bates <bates@stat.wisc.edu>
24    
25            * [r4778] R/AllGeneric.R: Check R version before defining generics for
26              primitives
27    
28    2007-09-13  Martin Maechler  <maechler@stat.math.ethz.ch>
29    
30            * R/denseMatrix.R (rcond): method
31            * R/sparseQR.R (rcond): method, use x or t(x)
32    
33    2007-09-12  Martin Maechler  <maechler@stat.math.ethz.ch>
34    
35            * R/dgeMatrix.R (rcond): method: work via qr.R() for non-square
36            matrices.
37            * R/sparseMatrix.R: Ditto for all other rcond() method definitions.
38    
39            * man/rcond.Rd: mention the more general definition, and add
40            example for non-square matrices.
41    
42            * man/chol.Rd: new file, for the S4 chol() generic and all methods.
43    
44    2007-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
45    
46            * R/sparseQR.R: add qr.R() method [to be used for rcond()]
47    
48    2007-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
49    
50            * R/Matrix.R ([<-): add (Matrix,missing,ANY,Matrix) etc
51            * tests/indexing.R: add new regression for the above cases.
52    
53    2007-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
54    
55            * src/Mutils.h (__sun): clause for alloca.h on Solaris
56    
57    2007-08-16  Martin Maechler  <maechler@stat.math.ethz.ch>
58    
59            * DESCRIPTION (Date, Version): 0.999375-2
60    
61    2007-08-15  Martin Maechler  <maechler@stat.math.ethz.ch>
62    
63            * R/HBMM.R (readMM): make work for pattern matrices as well
64    
65    2007-08-14 13:07  Douglas Bates <bates@stat.wisc.edu>
66    
67            * [r4730] src/Mutils.h: declare alloca
68            * [r4734] NAMESPACE, R/AllGeneric.R, R/Csparse.R, R/HBMM.R, R/Tsparse.R,
69              R/dgCMatrix.R, R/dgTMatrix.R, R/dsCMatrix.R, R/dsTMatrix.R,
70              man/externalFormats.Rd, src/Csparse.c, src/Csparse.h, src/DEPS.mkf,
71              src/HBMM.c, src/HBMM.h, src/Mutils.h, src/SOURCES_C.mkf, src/init.c,
72              src/mmio.c, src/mmio.h: Remove deprecated function writeHB and its
73              methods; switch writeMM to use CHOLMOD code; repair readMM
74    
75    2007-08-14  Martin Maechler  <maechler@stat.math.ethz.ch>
76    
77            * R/nearPD.R, man/nearPD.Rd (nearPD): new function built on Jens
78            Oehlschlaegel's ... result type still to be discussed!
79    
80    2007-08-10  Martin Maechler  <maechler@stat.math.ethz.ch>
81    
82            * man/image-methods.Rd: new, combining all image() methods
83    
84    2007-08-09  Martin Maechler  <maechler@stat.math.ethz.ch>
85    
86            * R/dgCMatrix.R: define qr() and lu() methods for "sparseMatrix"
87            to work via dgC...
88    
89            * R/Matrix.R (Matrix): special treatment for "table" (S3)
90    
91    2007-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
92    
93            * R/dgTMatrix.R (image): change defaults to
94                    aspect = "iso", colorkey = FALSE
95    
96    2007-08-06  Martin Maechler  <maechler@stat.math.ethz.ch>
97    
98            * src/dsyMatrix.c (dsyMatrix_matrix_mm): 'b' might be matrix;
99            must copy its *expanded* x slot before LAPACK call.
100    
101            * tests/matprod.R: test the last days' changes.
102    
103    2007-08-06 16:43  Douglas Bates <bates@stat.wisc.edu>
104    
105            * [r4712] inst/include/Matrix_stubs.c: Change R_cholmod_printf in stubs
106              as well as in sources
107            * [r4713] src/dsyMatrix.c: Duplicate the contents of the RHS before
108              Lapack call
109    
110    2007-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
111    
112            * R/Matrix.R (%*%, crossprod, tcrossprod): add method for
113                    ("Matrix", "matrix") which is needed in some cases.
114            Ditto for solve().
115    
116            * R/colSums.R (.as.dge.Fun): need ddenseMatrix methods to avoid
117            infinite recursion in dispatch for some cases.
118    
119    2007-08-02 08:48  Martin Maechler <maechler@stat.math.ethz.ch>
120    
121            * [r4693] src/chm_common.c: R_cholmod_printf() instead of Rprintf() just
122              so pointers match
123    
124    2007-08-02  Martin Maechler  <maechler@stat.math.ethz.ch>
125    
126            * DESCRIPTION (Date): set ready for release -- 0.999375-1
127    
128    2007-08-01 15:44  Douglas Bates <bates@stat.wisc.edu>
129    
130            * [r4686] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
131              src/chm_common.c, src/chm_common.h: Change API for
132              numeric_as_chm_dense and N_AS_CHM_DN
133    
134    2007-08-01  Martin Maechler  <maechler@stat.math.ethz.ch>
135    
136            * src/dtrMatrix.c (dtrMatrix_matrix_mm): fix dimensionality check (!)
137            * tests/matprod.R: regr.test for it
138    
139    2007-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
140    
141            * R/dMatrix.R: fix from Brian for   Math2(., digits = "missing")
142            * tests/group-methods.R: and regression-test it
143    
144    2007-07-19 19:45  Douglas Bates <bates@stat.wisc.edu>
145    
146            * [r4642] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
147              inst/include/cholmod.h, src/chm_common.c, src/init.c: Export
148              triplet_to_sparse, documentation, use typedefs
149    
150    2007-07-18  Martin Maechler  <maechler@stat.math.ethz.ch>
151    
152            * man/dpoMatrix-class.Rd: added 'corMatrix' example
153    
154            * src/dsyMatrix.[ch] (dsyMatrix_as_matrix): new 'keep_dimnames' arg
155            * src/dtrMatrix.[ch] (dtrMatrix_as_matrix): ditto
156            * src/init.c, R/dsyMatrix.R, R/dtrMatrix.R, R/lgTMatrix.R: ditto
157    
158            * R/lsparseMatrix.R: bug fix in "all" method
159            * R/Ops.R (.do.Logic.lsparse): "|" bug in borderline case
160    
161            * R/dsyMatrix.R (coerce->dsTMatrix): (i,j) slots should *not* have names
162            * R/ngTMatrix.R (coerce->ngTMatrix): ditto;
163                    + matrix |-> nMatrix coercion
164            * R/pMatrix.R: + setAs()  to dMatrix and from nMatrix
165            * man/pMatrix-class.Rd: ditto
166    
167            * R/Matrix.R (Summary): method for non-dMatrix
168    
169            * tests/Class+Meth.R (extraValid): new check about "dirty" slots
170            * tests/Class+Meth.R (tstMatrixClass): test norm(.);
171                    test all Summary methods.
172    
173    2007-07-16  Martin Maechler  <maechler@stat.math.ethz.ch>
174    
175            * R/dgeMatrix.R (norm, rcond): methods for 'matrix'
176    
177    2007-07-14  Martin Maechler  <maechler@stat.math.ethz.ch>
178    
179            * R/sparseMatrix.R (norm): simple methods for sparseMatrix
180    
181            * R/pMatrix.R (t?crossprod): methods for pMatrix
182    
183    2007-07-10  Douglas Bates  <bates@stat.wisc.edu>
184    
185            * src/dgeMatrix.c (dgeMatrix_colsums): Get the logic straight.
186    
187    2007-07-09 20:45  Douglas Bates <bates@stat.wisc.edu>
188    
189            * [r4579] src/dgeMatrix.c: Untangle horrible code in dgeMatrix_colsums
190              trying to fix a subtle bug - which has been somewhere else.
191    
192    2007-07-09 19:43  Martin Maechler <maechler@stat.math.ethz.ch>
193    
194            * [r4578] src/dgeMatrix.c: "cleaned" dgeMatrix_colsums() - but did not
195              solve the bug
196    
197    2007-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
198    
199            * src/dgCMatrix.c (compressed_to_TMatrix):
200    
201    2007-07-07  Martin Maechler  <maechler@stat.math.ethz.ch>
202    
203            * src/Csparse.c (Rsparse_validate): new, to have some validity
204            checking for RsparseMatrix
205            * src/dgCMatrix.c (xRMatrix_validate): ditto
206            * src/dtCMatrix.c (tRMatrix_validate): ditto
207    
208    2007-07-07  Douglas Bates <bates@stat.wisc.edu>
209    
210            * [r4567] R/AllClass.R: Slots already in RsparseMatrix were redefined in
211              lgRMatrix
212            * [r4568] DESCRIPTION: Prepare for bug-fix release
213            * [r4570] src/CHOLMOD/Check/cholmod_write.c: Include cholmod_matrixops.h
214              for declaration of cholmod_symmetry
215    
216    2007-07-06  Martin Maechler  <maechler@stat.math.ethz.ch>
217    
218            * DESCRIPTION (Version): 0.999375 merged into the trunk; ready for
219            release.
220    
221    2007-07-06 14:11  Douglas Bates <bates@stat.wisc.edu>
222    
223            * [r4559] src/iohb.c, src/iohb.h: Remove Harwell-Boeing input/output
224              functions - no longer used
225            * [r4560] src/HBMM.c, src/Mutils.c, src/dgTMatrix.c, src/dgeMatrix.c,
226              src/dspMatrix.c, src/dsyMatrix.c, src/dtCMatrix.c,
227              src/factorizations.c, src/sparseQR.c: Replace most calls to Calloc by
228              Alloca
229    
230    2007-07-06 13:14  Martin Maechler <maechler@stat.math.ethz.ch>
231    
232            * [r4558] inst/doc/Comparisons.Rnw, src/CHMfactor.c, src/Csparse.c,
233              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dense.c,
234              src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c, src/sparseQR.c,
235              src/t_gCMatrix_colSums.c: more R_CheckStack()s
236    
237    2007-07-05 18:12  Douglas Bates <bates@stat.wisc.edu>
238    
239            * [r4550] inst/include/Matrix.h: Add the macro N_AS_CHM_DN to "alloca"
240              the required amount of memory then call M_numeric_as_chm_dense.
241            * [r4556] src/Mutils.h, src/dgCMatrix.c: Define and use the Alloca macro
242              (like Calloc but calling alloca)
243    
244    2007-07-05  Martin Maechler  <maechler@stat.math.ethz.ch>
245    
246            * R/sparseMatrix.R (printSpMatrix): renamed from prSpMatrix()
247            and extended with more sophisticated 'col.names' option.
248            * NAMESPACE: export  printSparseMatrix()
249            * man/printSpMatrix.Rd: document, incl. examples
250    
251    2007-07-04 16:21  Douglas Bates <bates@stat.wisc.edu>
252    
253            * [r4543] src/cs_utils.c, src/cs_utils.h, src/dgCMatrix.c,
254              src/dtCMatrix.c, src/sparseQR.c: CSP typedef for *cs and macro
255              AS_CSP. API change - pass the empty structure to Matrix_as_cs.
256    
257    2007-07-04  Martin Maechler  <maechler@stat.math.ethz.ch>
258    
259            * DESCRIPTION (Version): 0.99875-4
260    
261            * tests/Class+Meth.R (tstMatrixClass): add dimnames, and hence test
262            some dimnames perservation.
263    
264            * R/dsTMatrix.R (t-method): keep dimnames
265            * R/dtTMatrix.R:  ditto
266    
267            * R/sparseMatrix.R (prSpMatrix): print colnames when non-trivial
268            and ncol(.) < 10
269    
270            * src/cs_utils.c: drop check_class() and use Matrix_check_class()
271            from Mutils.h
272    
273            * src/lgCMatrix.c ([ln]csc_to_matrix): no longer lose dimnames,
274            e.g. in as(<ngCMatrix>, "matrix")
275    
276    2007-07-01 13:27  Douglas Bates <bates@stat.wisc.edu>
277    
278            * [r4529] .: Create a branch for the API changes from the 0.99875
279              series to the 0.999375 series
280            * [r4530] DESCRIPTION, inst/include/Matrix.h,
281              inst/include/Matrix_stubs.c, src/CHMfactor.c, src/Csparse.c,
282              src/Mutils.h, src/Tsparse.c, src/chm_common.c, src/chm_common.h,
283              src/dense.c, src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c,
284              src/t_gCMatrix_colSums.c: API change - pass the empty structure to the
285              as_cholmod_x functions
286    
287    2007-06-30 09:05  Martin Maechler <maechler@stat.math.ethz.ch>
288    
289            * [r4527] trunk/Matrix/DESCRIPTION, trunk/Matrix/NAMESPACE,
290              trunk/Matrix/inst/doc/Comparisons.Rnw: add session- and hardware-info
291              to Comparisons
292    
293    >>>>>>> .merge-right.r4561
294    2007-06-29  Martin Maechler  <maechler@stat.math.ethz.ch>
295    
296            * DESCRIPTION (Version): 0.99875-3 ready to be released.
297    
298            * R/sparseMatrix.R (spMatrix): make spMatrix(3,4) working
299    
300            * R/AllGeneric.R: set "Math" (and "Math2") group generics in a way
301            that should also work in a future version of R.
302    
303    2007-06-21  Martin Maechler  <maechler@stat.math.ethz.ch>
304    
305            * NAMESPACE, R/AllClass.R: "xsparseVector" class union.
306    
307            * R/sparseVector.R: more *sparseVector coercions, notably for
308            non - double ones.
309    
310    2007-06-19  Martin Maechler  <maechler@stat.math.ethz.ch>
311    
312            * R/colSums.R: new file for all (col|row)(Sums|Means) methods,
313              notably the new ones building on the new .Call(.)s:
314    
315            * src/dgCMatrix.c (DEF_gCMatrix_COLSUMS): use to define
316            all 4 of [dlin]gCMatrix_colSums().
317    
318    2007-06-18 16:12  Douglas Bates <bates@stat.wisc.edu>
319    
320            * [r4472] src/Syms.h, src/init.c: Added Matrix_lengthSym
321            * [r4473] src/dgCMatrix.c: Modified dgCMatrix_colSums for sparseVector
322              result
323    
324    2007-06-16  Martin Maechler  <maechler@stat.math.ethz.ch>
325    
326            * R/kronecker.R: fix typo (could lead to inf.recursion)
327            * test/simple.R: testing that
328    
329            * R/sparseMatrix.R (prSpMatrix): change to be used as print()
330            method as well (which can have arguments, show() can't).
331    
332    2007-06-16 15:52  Douglas Bates <bates@stat.wisc.edu>
333    
334            * [r4466] R/dgCMatrix.R, src/dgCMatrix.c, src/dgCMatrix.h, src/init.c:
335              added dgCMatrix_colSums for [col,row][Sums,Means]
336    
337    2007-06-15 23:15  Douglas Bates <bates@stat.wisc.edu>
338    
339            * [r4460] R/sparseMatrix.R, man/dgCMatrix-class.Rd, src/dgCMatrix.c,
340              src/dgCMatrix.h, src/init.c: added lm.fit.sparse (unexported),
341              coercion of "factor" to "dgCMatrix" and dgCMatrix_cholsol
342            * [r4461] R/AllClass.R, man/sparseMatrix-class.Rd: draft "indicators"
343              class
344            * [r4463] R/sparseMatrix.R, man/dgCMatrix-class.Rd,
345              man/sparseMatrix-class.Rd: Don't need an "indicators" class - use the
346              row names to store the levels - duh!  Added an example.
347    
348    2007-06-14  Martin Maechler  <maechler@stat.math.ethz.ch>
349    
350            * src/Csparse.c (Csparse_validate): check for *repeated* entries
351            thanks to example from Christian Buchta; with a test here:
352            * tests/simple.R:
353    
354    2007-06-07  Martin Maechler  <maechler@stat.math.ethz.ch>
355    
356            * R/Auxiliaries.R (callGeneric): another fix, needed for some cases
357            of colSums(*, sparseResult = TRUE)
358    
359    2007-06-06  Martin Maechler  <maechler@stat.math.ethz.ch>
360    
361            * R/lsparseMatrix.R, R/ldenseMatrix.R (all, any): change default to
362            'na.rm = FALSE' as "everywhere" else in R.
363    
364    2007-06-05 Douglas Bates <bates@stat.wisc.edu>
365    
366            * [r4421] src/CSparse_install.sh: Modify for new organization of
367              CSparse package
368            * [r4425] src/UFsparse_download.sh: Update to version 3.0.0 of
369              SuiteSparse
370            * [r4426] src/Makefile: add ./UFconfig to the include path for
371              compilation
372            * [r4427] src/cs.[ch]: update to CSparse version 2.2.0
373            * [r4428] inst/doc/UFsparse/* src/{AMD,CHOLMOD,COLAMD}/*
374              src/UFconfig/UFconfig.h: Update to version 3.0.0 of SuiteSparse
375    
376    2007-06-05  Martin Maechler  <maechler@stat.math.ethz.ch>
377    
378            * R/Auxiliaries.R (emptyColnames): + argument msg.if.not.empty, used in
379            * R/sparseMatrix.R (prSpMatrix): now gives a message about
380            suppressed column names.
381    
382    2007-06-04 17:13  Douglas Bates <bates@stat.wisc.edu>
383    
384            * [r4418] src/Csparse.c, src/HBMM.c, src/Mutils.c, src/Mutils.h,
385              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dgCMatrix.c,
386              src/dgeMatrix.c, src/dpoMatrix.c, src/dpoMatrix.h, src/dppMatrix.c,
387              src/dppMatrix.h, src/dsCMatrix.c, src/dspMatrix.c, src/dspMatrix.h,
388              src/dsyMatrix.c, src/dsyMatrix.h, src/dtpMatrix.c, src/dtrMatrix.c:
389              Remove warnings after change to const char* CHAR
390    
391    2007-06-04 17:11  Douglas Bates <bates@stat.wisc.edu>
392    
393            * [r4417] inst/include/Matrix_stubs.c, inst/include/cholmod.h: Corrected
394              type of M_cholmod_ssmult
395    
396    2007-06-03 14:42  Douglas Bates <bates@stat.wisc.edu>
397    
398            * [r4412] inst/include/Matrix_stubs.c, inst/include/cholmod.h,
399              src/init.c: Yet another cholmod export - cholmod_ssmult
400    
401    2007-05-23  Martin Maechler  <maechler@stat.math.ethz.ch>
402    
403            * NAMESPACE: exported drop0(), since
404            * man/drop0.Rd: I have seen several cases, I really wanted to use
405            it, so our users may want too.
406    
407    2007-05-22  Martin Maechler  <maechler@stat.math.ethz.ch>
408    
409            * man/colSums.Rd: separately document colSums() etc, since these
410            have the extra argument 'sparseResult'.
411    
412  2007-05-21  Martin Maechler  <maechler@stat.math.ethz.ch>  2007-05-21  Martin Maechler  <maechler@stat.math.ethz.ch>
413    
414          * R/sparseMatrix.R (spMatrix): utility (T)sparse Matrix constructor;          * R/sparseMatrix.R (spMatrix): utility (T)sparse Matrix constructor;

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