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revision 1767, Mon Feb 5 16:53:17 2007 UTC revision 1987, Tue Jul 10 19:31:18 2007 UTC
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1    2007-07-10  Douglas Bates  <bates@stat.wisc.edu>
2    
3            * src/dgeMatrix.c (dgeMatrix_colsums): Get the logic straight.
4    
5    2007-07-09 20:45  Douglas Bates <bates@stat.wisc.edu>
6    
7            * [r4579] src/dgeMatrix.c: Untangle horrible code in dgeMatrix_colsums
8              to fix a subtle bug (Kurt Hornik and Ingo Feinerer)
9    
10    2007-07-09 19:43  Martin Maechler <maechler@stat.math.ethz.ch>
11    
12            * [r4578] src/dgeMatrix.c: "cleaned" dgeMatrix_colsums() - but did not
13              solve the bug
14    
15    2007-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
16    
17            * src/dgCMatrix.c (compressed_to_TMatrix):
18    
19    2007-07-07  Martin Maechler  <maechler@stat.math.ethz.ch>
20    
21            * src/Csparse.c (Rsparse_validate): new, to have some validity
22            checking for RsparseMatrix
23            * src/dgCMatrix.c (xRMatrix_validate): ditto
24            * src/dtCMatrix.c (tRMatrix_validate): ditto
25    
26    2007-07-07  Douglas Bates <bates@stat.wisc.edu>
27    
28            * [r4567] R/AllClass.R: Slots already in RsparseMatrix were redefined in
29              lgRMatrix
30            * [r4568] DESCRIPTION: Prepare for bug-fix release
31            * [r4570] src/CHOLMOD/Check/cholmod_write.c: Include cholmod_matrixops.h
32              for declaration of cholmod_symmetry
33    
34    2007-07-06  Martin Maechler  <maechler@stat.math.ethz.ch>
35    
36            * DESCRIPTION (Version): 0.999375 merged into the trunk; ready for
37            release.
38    
39    2007-07-06 14:11  Douglas Bates <bates@stat.wisc.edu>
40    
41            * [r4559] src/iohb.c, src/iohb.h: Remove Harwell-Boeing input/output
42              functions - no longer used
43            * [r4560] src/HBMM.c, src/Mutils.c, src/dgTMatrix.c, src/dgeMatrix.c,
44              src/dspMatrix.c, src/dsyMatrix.c, src/dtCMatrix.c,
45              src/factorizations.c, src/sparseQR.c: Replace most calls to Calloc by
46              Alloca
47    
48    2007-07-06 13:14  Martin Maechler <maechler@stat.math.ethz.ch>
49    
50            * [r4558] inst/doc/Comparisons.Rnw, src/CHMfactor.c, src/Csparse.c,
51              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dense.c,
52              src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c, src/sparseQR.c,
53              src/t_gCMatrix_colSums.c: more R_CheckStack()s
54    
55    2007-07-05 18:12  Douglas Bates <bates@stat.wisc.edu>
56    
57            * [r4550] inst/include/Matrix.h: Add the macro N_AS_CHM_DN to "alloca"
58              the required amount of memory then call M_numeric_as_chm_dense.
59            * [r4556] src/Mutils.h, src/dgCMatrix.c: Define and use the Alloca macro
60              (like Calloc but calling alloca)
61    
62    2007-07-05  Martin Maechler  <maechler@stat.math.ethz.ch>
63    
64            * R/sparseMatrix.R (printSpMatrix): renamed from prSpMatrix()
65            and extended with more sophisticated 'col.names' option.
66            * NAMESPACE: export  printSparseMatrix()
67            * man/printSpMatrix.Rd: document, incl. examples
68    
69    2007-07-04 16:21  Douglas Bates <bates@stat.wisc.edu>
70    
71            * [r4543] src/cs_utils.c, src/cs_utils.h, src/dgCMatrix.c,
72              src/dtCMatrix.c, src/sparseQR.c: CSP typedef for *cs and macro
73              AS_CSP. API change - pass the empty structure to Matrix_as_cs.
74    
75    2007-07-04  Martin Maechler  <maechler@stat.math.ethz.ch>
76    
77            * DESCRIPTION (Version): 0.99875-4
78    
79            * tests/Class+Meth.R (tstMatrixClass): add dimnames, and hence test
80            some dimnames perservation.
81    
82            * R/dsTMatrix.R (t-method): keep dimnames
83            * R/dtTMatrix.R:  ditto
84    
85            * R/sparseMatrix.R (prSpMatrix): print colnames when non-trivial
86            and ncol(.) < 10
87    
88            * src/cs_utils.c: drop check_class() and use Matrix_check_class()
89            from Mutils.h
90    
91            * src/lgCMatrix.c ([ln]csc_to_matrix): no longer lose dimnames,
92            e.g. in as(<ngCMatrix>, "matrix")
93    
94    2007-07-01 13:27  Douglas Bates <bates@stat.wisc.edu>
95    
96            * [r4529] .: Create a branch for the API changes from the 0.99875
97              series to the 0.999375 series
98            * [r4530] DESCRIPTION, inst/include/Matrix.h,
99              inst/include/Matrix_stubs.c, src/CHMfactor.c, src/Csparse.c,
100              src/Mutils.h, src/Tsparse.c, src/chm_common.c, src/chm_common.h,
101              src/dense.c, src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c,
102              src/t_gCMatrix_colSums.c: API change - pass the empty structure to the
103              as_cholmod_x functions
104    
105    2007-06-30 09:05  Martin Maechler <maechler@stat.math.ethz.ch>
106    
107            * [r4527] trunk/Matrix/DESCRIPTION, trunk/Matrix/NAMESPACE,
108              trunk/Matrix/inst/doc/Comparisons.Rnw: add session- and hardware-info
109              to Comparisons
110    
111    >>>>>>> .merge-right.r4561
112    2007-06-29  Martin Maechler  <maechler@stat.math.ethz.ch>
113    
114            * DESCRIPTION (Version): 0.99875-3 ready to be released.
115    
116            * R/sparseMatrix.R (spMatrix): make spMatrix(3,4) working
117    
118            * R/AllGeneric.R: set "Math" (and "Math2") group generics in a way
119            that should also work in a future version of R.
120    
121    2007-06-21  Martin Maechler  <maechler@stat.math.ethz.ch>
122    
123            * NAMESPACE, R/AllClass.R: "xsparseVector" class union.
124    
125            * R/sparseVector.R: more *sparseVector coercions, notably for
126            non - double ones.
127    
128    2007-06-19  Martin Maechler  <maechler@stat.math.ethz.ch>
129    
130            * R/colSums.R: new file for all (col|row)(Sums|Means) methods,
131              notably the new ones building on the new .Call(.)s:
132    
133            * src/dgCMatrix.c (DEF_gCMatrix_COLSUMS): use to define
134            all 4 of [dlin]gCMatrix_colSums().
135    
136    2007-06-18 16:12  Douglas Bates <bates@stat.wisc.edu>
137    
138            * [r4472] src/Syms.h, src/init.c: Added Matrix_lengthSym
139            * [r4473] src/dgCMatrix.c: Modified dgCMatrix_colSums for sparseVector
140              result
141    
142    2007-06-16  Martin Maechler  <maechler@stat.math.ethz.ch>
143    
144            * R/kronecker.R: fix typo (could lead to inf.recursion)
145            * test/simple.R: testing that
146    
147            * R/sparseMatrix.R (prSpMatrix): change to be used as print()
148            method as well (which can have arguments, show() can't).
149    
150    2007-06-16 15:52  Douglas Bates <bates@stat.wisc.edu>
151    
152            * [r4466] R/dgCMatrix.R, src/dgCMatrix.c, src/dgCMatrix.h, src/init.c:
153              added dgCMatrix_colSums for [col,row][Sums,Means]
154    
155    2007-06-15 23:15  Douglas Bates <bates@stat.wisc.edu>
156    
157            * [r4460] R/sparseMatrix.R, man/dgCMatrix-class.Rd, src/dgCMatrix.c,
158              src/dgCMatrix.h, src/init.c: added lm.fit.sparse (unexported),
159              coercion of "factor" to "dgCMatrix" and dgCMatrix_cholsol
160            * [r4461] R/AllClass.R, man/sparseMatrix-class.Rd: draft "indicators"
161              class
162            * [r4463] R/sparseMatrix.R, man/dgCMatrix-class.Rd,
163              man/sparseMatrix-class.Rd: Don't need an "indicators" class - use the
164              row names to store the levels - duh!  Added an example.
165    
166    2007-06-14  Martin Maechler  <maechler@stat.math.ethz.ch>
167    
168            * src/Csparse.c (Csparse_validate): check for *repeated* entries
169            thanks to example from Christian Buchta; with a test here:
170            * tests/simple.R:
171    
172    2007-06-07  Martin Maechler  <maechler@stat.math.ethz.ch>
173    
174            * R/Auxiliaries.R (callGeneric): another fix, needed for some cases
175            of colSums(*, sparseResult = TRUE)
176    
177    2007-06-06  Martin Maechler  <maechler@stat.math.ethz.ch>
178    
179            * R/lsparseMatrix.R, R/ldenseMatrix.R (all, any): change default to
180            'na.rm = FALSE' as "everywhere" else in R.
181    
182    2007-06-05 Douglas Bates <bates@stat.wisc.edu>
183    
184            * [r4421] src/CSparse_install.sh: Modify for new organization of
185              CSparse package
186            * [r4425] src/UFsparse_download.sh: Update to version 3.0.0 of
187              SuiteSparse
188            * [r4426] src/Makefile: add ./UFconfig to the include path for
189              compilation
190            * [r4427] src/cs.[ch]: update to CSparse version 2.2.0
191            * [r4428] inst/doc/UFsparse/* src/{AMD,CHOLMOD,COLAMD}/*
192              src/UFconfig/UFconfig.h: Update to version 3.0.0 of SuiteSparse
193    
194    2007-06-05  Martin Maechler  <maechler@stat.math.ethz.ch>
195    
196            * R/Auxiliaries.R (emptyColnames): + argument msg.if.not.empty, used in
197            * R/sparseMatrix.R (prSpMatrix): now gives a message about
198            suppressed column names.
199    
200    2007-06-04 17:13  Douglas Bates <bates@stat.wisc.edu>
201    
202            * [r4418] src/Csparse.c, src/HBMM.c, src/Mutils.c, src/Mutils.h,
203              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dgCMatrix.c,
204              src/dgeMatrix.c, src/dpoMatrix.c, src/dpoMatrix.h, src/dppMatrix.c,
205              src/dppMatrix.h, src/dsCMatrix.c, src/dspMatrix.c, src/dspMatrix.h,
206              src/dsyMatrix.c, src/dsyMatrix.h, src/dtpMatrix.c, src/dtrMatrix.c:
207              Remove warnings after change to const char* CHAR
208    
209    2007-06-04 17:11  Douglas Bates <bates@stat.wisc.edu>
210    
211            * [r4417] inst/include/Matrix_stubs.c, inst/include/cholmod.h: Corrected
212              type of M_cholmod_ssmult
213    
214    2007-06-03 14:42  Douglas Bates <bates@stat.wisc.edu>
215    
216            * [r4412] inst/include/Matrix_stubs.c, inst/include/cholmod.h,
217              src/init.c: Yet another cholmod export - cholmod_ssmult
218    
219    2007-05-23  Martin Maechler  <maechler@stat.math.ethz.ch>
220    
221            * NAMESPACE: exported drop0(), since
222            * man/drop0.Rd: I have seen several cases, I really wanted to use
223            it, so our users may want too.
224    
225    2007-05-22  Martin Maechler  <maechler@stat.math.ethz.ch>
226    
227            * man/colSums.Rd: separately document colSums() etc, since these
228            have the extra argument 'sparseResult'.
229    
230    2007-05-21  Martin Maechler  <maechler@stat.math.ethz.ch>
231    
232            * R/sparseMatrix.R (spMatrix): utility (T)sparse Matrix constructor;
233            * man/spMatrix.Rd: docu., including examples
234    
235            * R/Auxiliaries.R (sp.colMeans): etc, using a patched callGeneric(),
236            in order to make colMeans() etc fast *and* correct.
237            * R/sparseVector.R (replSPvec): "[<-" functionality for
238            sparseVectors; tested in
239            * tests/simple.R:
240    
241    2007-05-19  Martin Maechler  <maechler@stat.math.ethz.ch>
242    
243            * R/sparseMatrix.R (print.sparseSummary): and summary() method for
244            (very) sparse Matrices; output similar to Matlab's print().
245    
246    2007-05-17  Douglas Bates  <bates@stat.wisc.edu>
247    
248            * src/HBMM.c (Matrix_writeMatrixMarket): Write 1-based, not
249            0-based, indices (Jose Quesada <quesada@gmail.com>).
250    
251    2007-05-16  Douglas Bates  <bates@stat.wisc.edu>
252    
253            * R/CHMfactor.R: Added solve methods for a CHMfactor object.
254    
255    2007-05-16  Martin Maechler  <maechler@stat.math.ethz.ch>
256    
257            * R/Auxiliaries.R (sparsapply): new utility, much faster than
258            tapply1() for large sparse matrices.
259    
260    2007-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
261    
262            * R/Matrix.R (dim<-): reshape now via sparseVector.
263    
264            * R/sparseVector.R: methods and function for
265            * R/AllClass.R: new "sparseVector" class and daughters.
266            * NAMESPACE: export new classes
267    
268    2007-05-14  Martin Maechler  <maechler@stat.math.ethz.ch>
269    
270            * DESCRIPTION (Version): 0.99875-1
271            * src/Makefile.win: also remove Lapack code from here (cf. 04-25).
272    
273    2007-05-11  Martin Maechler  <maechler@stat.math.ethz.ch>
274    
275            * R/Tsparse.R ([, Tsparse): fix last case: *duplicated*, symmetric
276            indexing
277            * tests/indexing.R: test set for that.
278    
279    2007-05-08  Martin Maechler  <maechler@stat.math.ethz.ch>
280    
281            * R/Tsparse.R (replTmat): fix the case of *duplicated* index
282            entries.
283            * tests/indexing.R(out): add regression test for it
284    
285    2007-04-30  Martin Maechler  <maechler@stat.math.ethz.ch>
286    
287            * R/(l(dense|sparse))?Matrix.R (!): use 'x', not 'e1' as argument
288            name for "!" method definitions.
289    
290    2007-04-26  Martin Maechler  <maechler@stat.math.ethz.ch>
291    
292            * R/Tsparse.R (intI): new utility, used for "[" :
293                    Cleanup up there, and fixes for duplicated indices - more TODO!
294    
295            * tests/indexing.R(out): more tests
296    
297    2007-04-25  Douglas Bates  <bates@stat.wisc.edu>
298    
299            * DESCRIPTION,src/Makefile: require R>= 2.5.0 and remove Lapack
300            code that is now part of the R Lapack library.
301    
302            * src/init.c,inst/include/{Matrix_stubs.c,cholmod.h}:export
303            cholmod_factorize_p (used in lme4 for GLMMs and NLMMs).
304    
305    2007-04-21  Martin Maechler  <maechler@stat.math.ethz.ch>
306    
307            * R/Matrix.R (image): method for all Matrices, not just sparse ones.
308    
309    2007-04-17  Martin Maechler  <maechler@stat.math.ethz.ch>
310    
311            * R/Auxiliaries.R (tapply1): unname(.) -> colSums() etc don't end
312            up with extraneous names '0'...'<n-1>'
313    
314    2007-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
315    
316            * R/dgTMatrix.R (mat2dgT): care about NAs
317    
318    2007-04-11  Martin Maechler  <maechler@stat.math.ethz.ch>
319    
320            * R/kronecker.R: triangularity preserving methods
321    
322    2007-03-27  Martin Maechler  <maechler@stat.math.ethz.ch>
323    
324            * R/kronecker.R: new file collecting kronecker() methods in one
325                    place.  Goal: become much faster!
326    
327    2007-03-23  Martin Maechler  <maechler@stat.math.ethz.ch>
328    
329            * src/dtCMatrix.c (dtCMatrix_solve): use the new code from Kasper
330            Kristensen based cs_spsolve() instead of _lsolve & _usolve which
331            can be much faster.
332    
333            * tests/matprod.R: add regression tests for these (upper & lower).
334    
335    2007-03-19  Martin Maechler  <maechler@stat.math.ethz.ch>
336    
337            * R/Matrix.R (diff): method for our Matrices.
338    
339            * R/sparseMatrix.R (isDiagonal): check dim()!
340    
341    2007-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
342    
343            * R/Matrix.R (dim<-): new method for "reshape()" built on a
344            proposal from Tamas Papp.
345    
346    2007-03-16  Martin Maechler  <maechler@stat.math.ethz.ch>
347    
348            * R/AllGeneric.R: remove all  if(!isGeneric(.))  clauses
349    
350            * R/zzz.R (.onLoad, .onUnload): do *not* leave bind_activation(TRUE);
351            rather define and export  cBind() and rBind() only.
352            --> useRs *must* change code that used to have cbind()/rbind() !!
353    
354            * R/bind.R: change tests from cbind() to cBind() and similarly to rBind()
355            * R/bind.Rout.save: ditto
356    
357    2007-02-16  Douglas Bates  <bates@r-project.org>
358    
359            * DESCRIPTION (Date, Version): 0.9975-11 with new date
360            * src/dgCMatrix.c (R_to_CMatrix, compressed_to_TMatrix): remove
361            const modifier on declaration of the array 'valid'
362    
363    2007-02-12  Douglas Bates  <bates@stat.wisc.edu>
364    
365            * R/CHMfactor.R: Add image method (coercion to sparseMatrix).
366    
367  2007-02-05  Martin Maechler  <maechler@stat.math.ethz.ch>  2007-02-05  Martin Maechler  <maechler@stat.math.ethz.ch>
368    
369            * DESCRIPTION (Date, Version): 0.9975-10 with new date.
370    
371          * R/Ops.R (Arith): make sure Csparse o Csparse also works for e.g. ntCMatrix          * R/Ops.R (Arith): make sure Csparse o Csparse also works for e.g. ntCMatrix
372          * tests/simple.R: test the above and some of these coercions:          * tests/simple.R: test the above and some of these coercions:
373    

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