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revision 1767, Mon Feb 5 16:53:17 2007 UTC revision 1975, Mon Jul 9 20:52:50 2007 UTC
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1    2007-07-09 20:45  Douglas Bates <bates@stat.wisc.edu>
2    
3            * [r4579] src/dgeMatrix.c: Untangle horrible code in dgeMatrix_colsums
4              to fix a subtle bug (Kurt Hornik and Ingo Feinerer)
5    
6    2007-07-09 19:43  Martin Maechler <maechler@stat.math.ethz.ch>
7    
8            * [r4578] src/dgeMatrix.c: "cleaned" dgeMatrix_colsums() - but did not
9              solve the bug
10    
11    2007-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
12    
13            * src/dgCMatrix.c (compressed_to_TMatrix):
14    
15    2007-07-07  Martin Maechler  <maechler@stat.math.ethz.ch>
16    
17            * src/Csparse.c (Rsparse_validate): new, to have some validity
18            checking for RsparseMatrix
19            * src/dgCMatrix.c (xRMatrix_validate): ditto
20            * src/dtCMatrix.c (tRMatrix_validate): ditto
21    
22    2007-07-07  Douglas Bates <bates@stat.wisc.edu>
23    
24            * [r4567] R/AllClass.R: Slots already in RsparseMatrix were redefined in
25              lgRMatrix
26            * [r4568] DESCRIPTION: Prepare for bug-fix release
27            * [r4570] src/CHOLMOD/Check/cholmod_write.c: Include cholmod_matrixops.h
28              for declaration of cholmod_symmetry
29    
30    2007-07-06  Martin Maechler  <maechler@stat.math.ethz.ch>
31    
32            * DESCRIPTION (Version): 0.999375 merged into the trunk; ready for
33            release.
34    
35    2007-07-06 14:11  Douglas Bates <bates@stat.wisc.edu>
36    
37            * [r4559] src/iohb.c, src/iohb.h: Remove Harwell-Boeing input/output
38              functions - no longer used
39            * [r4560] src/HBMM.c, src/Mutils.c, src/dgTMatrix.c, src/dgeMatrix.c,
40              src/dspMatrix.c, src/dsyMatrix.c, src/dtCMatrix.c,
41              src/factorizations.c, src/sparseQR.c: Replace most calls to Calloc by
42              Alloca
43    
44    2007-07-06 13:14  Martin Maechler <maechler@stat.math.ethz.ch>
45    
46            * [r4558] inst/doc/Comparisons.Rnw, src/CHMfactor.c, src/Csparse.c,
47              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dense.c,
48              src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c, src/sparseQR.c,
49              src/t_gCMatrix_colSums.c: more R_CheckStack()s
50    
51    2007-07-05 18:12  Douglas Bates <bates@stat.wisc.edu>
52    
53            * [r4550] inst/include/Matrix.h: Add the macro N_AS_CHM_DN to "alloca"
54              the required amount of memory then call M_numeric_as_chm_dense.
55            * [r4556] src/Mutils.h, src/dgCMatrix.c: Define and use the Alloca macro
56              (like Calloc but calling alloca)
57    
58    2007-07-05  Martin Maechler  <maechler@stat.math.ethz.ch>
59    
60            * R/sparseMatrix.R (printSpMatrix): renamed from prSpMatrix()
61            and extended with more sophisticated 'col.names' option.
62            * NAMESPACE: export  printSparseMatrix()
63            * man/printSpMatrix.Rd: document, incl. examples
64    
65    2007-07-04 16:21  Douglas Bates <bates@stat.wisc.edu>
66    
67            * [r4543] src/cs_utils.c, src/cs_utils.h, src/dgCMatrix.c,
68              src/dtCMatrix.c, src/sparseQR.c: CSP typedef for *cs and macro
69              AS_CSP. API change - pass the empty structure to Matrix_as_cs.
70    
71    2007-07-04  Martin Maechler  <maechler@stat.math.ethz.ch>
72    
73            * DESCRIPTION (Version): 0.99875-4
74    
75            * tests/Class+Meth.R (tstMatrixClass): add dimnames, and hence test
76            some dimnames perservation.
77    
78            * R/dsTMatrix.R (t-method): keep dimnames
79            * R/dtTMatrix.R:  ditto
80    
81            * R/sparseMatrix.R (prSpMatrix): print colnames when non-trivial
82            and ncol(.) < 10
83    
84            * src/cs_utils.c: drop check_class() and use Matrix_check_class()
85            from Mutils.h
86    
87            * src/lgCMatrix.c ([ln]csc_to_matrix): no longer lose dimnames,
88            e.g. in as(<ngCMatrix>, "matrix")
89    
90    2007-07-01 13:27  Douglas Bates <bates@stat.wisc.edu>
91    
92            * [r4529] .: Create a branch for the API changes from the 0.99875
93              series to the 0.999375 series
94            * [r4530] DESCRIPTION, inst/include/Matrix.h,
95              inst/include/Matrix_stubs.c, src/CHMfactor.c, src/Csparse.c,
96              src/Mutils.h, src/Tsparse.c, src/chm_common.c, src/chm_common.h,
97              src/dense.c, src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c,
98              src/t_gCMatrix_colSums.c: API change - pass the empty structure to the
99              as_cholmod_x functions
100    
101    2007-06-30 09:05  Martin Maechler <maechler@stat.math.ethz.ch>
102    
103            * [r4527] trunk/Matrix/DESCRIPTION, trunk/Matrix/NAMESPACE,
104              trunk/Matrix/inst/doc/Comparisons.Rnw: add session- and hardware-info
105              to Comparisons
106    
107    >>>>>>> .merge-right.r4561
108    2007-06-29  Martin Maechler  <maechler@stat.math.ethz.ch>
109    
110            * DESCRIPTION (Version): 0.99875-3 ready to be released.
111    
112            * R/sparseMatrix.R (spMatrix): make spMatrix(3,4) working
113    
114            * R/AllGeneric.R: set "Math" (and "Math2") group generics in a way
115            that should also work in a future version of R.
116    
117    2007-06-21  Martin Maechler  <maechler@stat.math.ethz.ch>
118    
119            * NAMESPACE, R/AllClass.R: "xsparseVector" class union.
120    
121            * R/sparseVector.R: more *sparseVector coercions, notably for
122            non - double ones.
123    
124    2007-06-19  Martin Maechler  <maechler@stat.math.ethz.ch>
125    
126            * R/colSums.R: new file for all (col|row)(Sums|Means) methods,
127              notably the new ones building on the new .Call(.)s:
128    
129            * src/dgCMatrix.c (DEF_gCMatrix_COLSUMS): use to define
130            all 4 of [dlin]gCMatrix_colSums().
131    
132    2007-06-18 16:12  Douglas Bates <bates@stat.wisc.edu>
133    
134            * [r4472] src/Syms.h, src/init.c: Added Matrix_lengthSym
135            * [r4473] src/dgCMatrix.c: Modified dgCMatrix_colSums for sparseVector
136              result
137    
138    2007-06-16  Martin Maechler  <maechler@stat.math.ethz.ch>
139    
140            * R/kronecker.R: fix typo (could lead to inf.recursion)
141            * test/simple.R: testing that
142    
143            * R/sparseMatrix.R (prSpMatrix): change to be used as print()
144            method as well (which can have arguments, show() can't).
145    
146    2007-06-16 15:52  Douglas Bates <bates@stat.wisc.edu>
147    
148            * [r4466] R/dgCMatrix.R, src/dgCMatrix.c, src/dgCMatrix.h, src/init.c:
149              added dgCMatrix_colSums for [col,row][Sums,Means]
150    
151    2007-06-15 23:15  Douglas Bates <bates@stat.wisc.edu>
152    
153            * [r4460] R/sparseMatrix.R, man/dgCMatrix-class.Rd, src/dgCMatrix.c,
154              src/dgCMatrix.h, src/init.c: added lm.fit.sparse (unexported),
155              coercion of "factor" to "dgCMatrix" and dgCMatrix_cholsol
156            * [r4461] R/AllClass.R, man/sparseMatrix-class.Rd: draft "indicators"
157              class
158            * [r4463] R/sparseMatrix.R, man/dgCMatrix-class.Rd,
159              man/sparseMatrix-class.Rd: Don't need an "indicators" class - use the
160              row names to store the levels - duh!  Added an example.
161    
162    2007-06-14  Martin Maechler  <maechler@stat.math.ethz.ch>
163    
164            * src/Csparse.c (Csparse_validate): check for *repeated* entries
165            thanks to example from Christian Buchta; with a test here:
166            * tests/simple.R:
167    
168    2007-06-07  Martin Maechler  <maechler@stat.math.ethz.ch>
169    
170            * R/Auxiliaries.R (callGeneric): another fix, needed for some cases
171            of colSums(*, sparseResult = TRUE)
172    
173    2007-06-06  Martin Maechler  <maechler@stat.math.ethz.ch>
174    
175            * R/lsparseMatrix.R, R/ldenseMatrix.R (all, any): change default to
176            'na.rm = FALSE' as "everywhere" else in R.
177    
178    2007-06-05 Douglas Bates <bates@stat.wisc.edu>
179    
180            * [r4421] src/CSparse_install.sh: Modify for new organization of
181              CSparse package
182            * [r4425] src/UFsparse_download.sh: Update to version 3.0.0 of
183              SuiteSparse
184            * [r4426] src/Makefile: add ./UFconfig to the include path for
185              compilation
186            * [r4427] src/cs.[ch]: update to CSparse version 2.2.0
187            * [r4428] inst/doc/UFsparse/* src/{AMD,CHOLMOD,COLAMD}/*
188              src/UFconfig/UFconfig.h: Update to version 3.0.0 of SuiteSparse
189    
190    2007-06-05  Martin Maechler  <maechler@stat.math.ethz.ch>
191    
192            * R/Auxiliaries.R (emptyColnames): + argument msg.if.not.empty, used in
193            * R/sparseMatrix.R (prSpMatrix): now gives a message about
194            suppressed column names.
195    
196    2007-06-04 17:13  Douglas Bates <bates@stat.wisc.edu>
197    
198            * [r4418] src/Csparse.c, src/HBMM.c, src/Mutils.c, src/Mutils.h,
199              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dgCMatrix.c,
200              src/dgeMatrix.c, src/dpoMatrix.c, src/dpoMatrix.h, src/dppMatrix.c,
201              src/dppMatrix.h, src/dsCMatrix.c, src/dspMatrix.c, src/dspMatrix.h,
202              src/dsyMatrix.c, src/dsyMatrix.h, src/dtpMatrix.c, src/dtrMatrix.c:
203              Remove warnings after change to const char* CHAR
204    
205    2007-06-04 17:11  Douglas Bates <bates@stat.wisc.edu>
206    
207            * [r4417] inst/include/Matrix_stubs.c, inst/include/cholmod.h: Corrected
208              type of M_cholmod_ssmult
209    
210    2007-06-03 14:42  Douglas Bates <bates@stat.wisc.edu>
211    
212            * [r4412] inst/include/Matrix_stubs.c, inst/include/cholmod.h,
213              src/init.c: Yet another cholmod export - cholmod_ssmult
214    
215    2007-05-23  Martin Maechler  <maechler@stat.math.ethz.ch>
216    
217            * NAMESPACE: exported drop0(), since
218            * man/drop0.Rd: I have seen several cases, I really wanted to use
219            it, so our users may want too.
220    
221    2007-05-22  Martin Maechler  <maechler@stat.math.ethz.ch>
222    
223            * man/colSums.Rd: separately document colSums() etc, since these
224            have the extra argument 'sparseResult'.
225    
226    2007-05-21  Martin Maechler  <maechler@stat.math.ethz.ch>
227    
228            * R/sparseMatrix.R (spMatrix): utility (T)sparse Matrix constructor;
229            * man/spMatrix.Rd: docu., including examples
230    
231            * R/Auxiliaries.R (sp.colMeans): etc, using a patched callGeneric(),
232            in order to make colMeans() etc fast *and* correct.
233            * R/sparseVector.R (replSPvec): "[<-" functionality for
234            sparseVectors; tested in
235            * tests/simple.R:
236    
237    2007-05-19  Martin Maechler  <maechler@stat.math.ethz.ch>
238    
239            * R/sparseMatrix.R (print.sparseSummary): and summary() method for
240            (very) sparse Matrices; output similar to Matlab's print().
241    
242    2007-05-17  Douglas Bates  <bates@stat.wisc.edu>
243    
244            * src/HBMM.c (Matrix_writeMatrixMarket): Write 1-based, not
245            0-based, indices (Jose Quesada <quesada@gmail.com>).
246    
247    2007-05-16  Douglas Bates  <bates@stat.wisc.edu>
248    
249            * R/CHMfactor.R: Added solve methods for a CHMfactor object.
250    
251    2007-05-16  Martin Maechler  <maechler@stat.math.ethz.ch>
252    
253            * R/Auxiliaries.R (sparsapply): new utility, much faster than
254            tapply1() for large sparse matrices.
255    
256    2007-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
257    
258            * R/Matrix.R (dim<-): reshape now via sparseVector.
259    
260            * R/sparseVector.R: methods and function for
261            * R/AllClass.R: new "sparseVector" class and daughters.
262            * NAMESPACE: export new classes
263    
264    2007-05-14  Martin Maechler  <maechler@stat.math.ethz.ch>
265    
266            * DESCRIPTION (Version): 0.99875-1
267            * src/Makefile.win: also remove Lapack code from here (cf. 04-25).
268    
269    2007-05-11  Martin Maechler  <maechler@stat.math.ethz.ch>
270    
271            * R/Tsparse.R ([, Tsparse): fix last case: *duplicated*, symmetric
272            indexing
273            * tests/indexing.R: test set for that.
274    
275    2007-05-08  Martin Maechler  <maechler@stat.math.ethz.ch>
276    
277            * R/Tsparse.R (replTmat): fix the case of *duplicated* index
278            entries.
279            * tests/indexing.R(out): add regression test for it
280    
281    2007-04-30  Martin Maechler  <maechler@stat.math.ethz.ch>
282    
283            * R/(l(dense|sparse))?Matrix.R (!): use 'x', not 'e1' as argument
284            name for "!" method definitions.
285    
286    2007-04-26  Martin Maechler  <maechler@stat.math.ethz.ch>
287    
288            * R/Tsparse.R (intI): new utility, used for "[" :
289                    Cleanup up there, and fixes for duplicated indices - more TODO!
290    
291            * tests/indexing.R(out): more tests
292    
293    2007-04-25  Douglas Bates  <bates@stat.wisc.edu>
294    
295            * DESCRIPTION,src/Makefile: require R>= 2.5.0 and remove Lapack
296            code that is now part of the R Lapack library.
297    
298            * src/init.c,inst/include/{Matrix_stubs.c,cholmod.h}:export
299            cholmod_factorize_p (used in lme4 for GLMMs and NLMMs).
300    
301    2007-04-21  Martin Maechler  <maechler@stat.math.ethz.ch>
302    
303            * R/Matrix.R (image): method for all Matrices, not just sparse ones.
304    
305    2007-04-17  Martin Maechler  <maechler@stat.math.ethz.ch>
306    
307            * R/Auxiliaries.R (tapply1): unname(.) -> colSums() etc don't end
308            up with extraneous names '0'...'<n-1>'
309    
310    2007-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
311    
312            * R/dgTMatrix.R (mat2dgT): care about NAs
313    
314    2007-04-11  Martin Maechler  <maechler@stat.math.ethz.ch>
315    
316            * R/kronecker.R: triangularity preserving methods
317    
318    2007-03-27  Martin Maechler  <maechler@stat.math.ethz.ch>
319    
320            * R/kronecker.R: new file collecting kronecker() methods in one
321                    place.  Goal: become much faster!
322    
323    2007-03-23  Martin Maechler  <maechler@stat.math.ethz.ch>
324    
325            * src/dtCMatrix.c (dtCMatrix_solve): use the new code from Kasper
326            Kristensen based cs_spsolve() instead of _lsolve & _usolve which
327            can be much faster.
328    
329            * tests/matprod.R: add regression tests for these (upper & lower).
330    
331    2007-03-19  Martin Maechler  <maechler@stat.math.ethz.ch>
332    
333            * R/Matrix.R (diff): method for our Matrices.
334    
335            * R/sparseMatrix.R (isDiagonal): check dim()!
336    
337    2007-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
338    
339            * R/Matrix.R (dim<-): new method for "reshape()" built on a
340            proposal from Tamas Papp.
341    
342    2007-03-16  Martin Maechler  <maechler@stat.math.ethz.ch>
343    
344            * R/AllGeneric.R: remove all  if(!isGeneric(.))  clauses
345    
346            * R/zzz.R (.onLoad, .onUnload): do *not* leave bind_activation(TRUE);
347            rather define and export  cBind() and rBind() only.
348            --> useRs *must* change code that used to have cbind()/rbind() !!
349    
350            * R/bind.R: change tests from cbind() to cBind() and similarly to rBind()
351            * R/bind.Rout.save: ditto
352    
353    2007-02-16  Douglas Bates  <bates@r-project.org>
354    
355            * DESCRIPTION (Date, Version): 0.9975-11 with new date
356            * src/dgCMatrix.c (R_to_CMatrix, compressed_to_TMatrix): remove
357            const modifier on declaration of the array 'valid'
358    
359    2007-02-12  Douglas Bates  <bates@stat.wisc.edu>
360    
361            * R/CHMfactor.R: Add image method (coercion to sparseMatrix).
362    
363  2007-02-05  Martin Maechler  <maechler@stat.math.ethz.ch>  2007-02-05  Martin Maechler  <maechler@stat.math.ethz.ch>
364    
365            * DESCRIPTION (Date, Version): 0.9975-10 with new date.
366    
367          * 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
368          * tests/simple.R: test the above and some of these coercions:          * tests/simple.R: test the above and some of these coercions:
369    

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