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revision 1768, Mon Feb 5 17:49:54 2007 UTC revision 2011, Fri Jul 20 12:56:10 2007 UTC
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1    2007-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * R/dMatrix.R: fix from Brian for   Math2(., digits = "missing")
4            * tests/group-methods.R: and regression-test it
5    
6    2007-07-19 19:45  Douglas Bates <bates@stat.wisc.edu>
7    
8            * [r4642] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
9              inst/include/cholmod.h, src/chm_common.c, src/init.c: Export
10              triplet_to_sparse, documentation, use typedefs
11    
12    2007-07-18  Martin Maechler  <maechler@stat.math.ethz.ch>
13    
14            * man/dpoMatrix-class.Rd: added 'corMatrix' example
15    
16            * src/dsyMatrix.[ch] (dsyMatrix_as_matrix): new 'keep_dimnames' arg
17            * src/dtrMatrix.[ch] (dtrMatrix_as_matrix): ditto
18            * src/init.c, R/dsyMatrix.R, R/dtrMatrix.R, R/lgTMatrix.R: ditto
19    
20            * R/lsparseMatrix.R: bug fix in "all" method
21            * R/Ops.R (.do.Logic.lsparse): "|" bug in borderline case
22    
23            * R/dsyMatrix.R (coerce->dsTMatrix): (i,j) slots should *not* have names
24            * R/ngTMatrix.R (coerce->ngTMatrix): ditto;
25                    + matrix |-> nMatrix coercion
26            * R/pMatrix.R: + setAs()  to dMatrix and from nMatrix
27            * man/pMatrix-class.Rd: ditto
28    
29            * R/Matrix.R (Summary): method for non-dMatrix
30    
31            * tests/Class+Meth.R (extraValid): new check about "dirty" slots
32            * tests/Class+Meth.R (tstMatrixClass): test norm(.);
33                    test all Summary methods.
34    
35    2007-07-16  Martin Maechler  <maechler@stat.math.ethz.ch>
36    
37            * R/dgeMatrix.R (norm, rcond): methods for 'matrix'
38    
39    2007-07-14  Martin Maechler  <maechler@stat.math.ethz.ch>
40    
41            * R/sparseMatrix.R (norm): simple methods for sparseMatrix
42    
43            * R/pMatrix.R (t?crossprod): methods for pMatrix
44    
45    2007-07-10  Douglas Bates  <bates@stat.wisc.edu>
46    
47            * src/dgeMatrix.c (dgeMatrix_colsums): Get the logic straight.
48    
49    2007-07-09 20:45  Douglas Bates <bates@stat.wisc.edu>
50    
51            * [r4579] src/dgeMatrix.c: Untangle horrible code in dgeMatrix_colsums
52              trying to fix a subtle bug - which has been somewhere else.
53    
54    2007-07-09 19:43  Martin Maechler <maechler@stat.math.ethz.ch>
55    
56            * [r4578] src/dgeMatrix.c: "cleaned" dgeMatrix_colsums() - but did not
57              solve the bug
58    
59    2007-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
60    
61            * src/dgCMatrix.c (compressed_to_TMatrix):
62    
63    2007-07-07  Martin Maechler  <maechler@stat.math.ethz.ch>
64    
65            * src/Csparse.c (Rsparse_validate): new, to have some validity
66            checking for RsparseMatrix
67            * src/dgCMatrix.c (xRMatrix_validate): ditto
68            * src/dtCMatrix.c (tRMatrix_validate): ditto
69    
70    2007-07-07  Douglas Bates <bates@stat.wisc.edu>
71    
72            * [r4567] R/AllClass.R: Slots already in RsparseMatrix were redefined in
73              lgRMatrix
74            * [r4568] DESCRIPTION: Prepare for bug-fix release
75            * [r4570] src/CHOLMOD/Check/cholmod_write.c: Include cholmod_matrixops.h
76              for declaration of cholmod_symmetry
77    
78    2007-07-06  Martin Maechler  <maechler@stat.math.ethz.ch>
79    
80            * DESCRIPTION (Version): 0.999375 merged into the trunk; ready for
81            release.
82    
83    2007-07-06 14:11  Douglas Bates <bates@stat.wisc.edu>
84    
85            * [r4559] src/iohb.c, src/iohb.h: Remove Harwell-Boeing input/output
86              functions - no longer used
87            * [r4560] src/HBMM.c, src/Mutils.c, src/dgTMatrix.c, src/dgeMatrix.c,
88              src/dspMatrix.c, src/dsyMatrix.c, src/dtCMatrix.c,
89              src/factorizations.c, src/sparseQR.c: Replace most calls to Calloc by
90              Alloca
91    
92    2007-07-06 13:14  Martin Maechler <maechler@stat.math.ethz.ch>
93    
94            * [r4558] inst/doc/Comparisons.Rnw, src/CHMfactor.c, src/Csparse.c,
95              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dense.c,
96              src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c, src/sparseQR.c,
97              src/t_gCMatrix_colSums.c: more R_CheckStack()s
98    
99    2007-07-05 18:12  Douglas Bates <bates@stat.wisc.edu>
100    
101            * [r4550] inst/include/Matrix.h: Add the macro N_AS_CHM_DN to "alloca"
102              the required amount of memory then call M_numeric_as_chm_dense.
103            * [r4556] src/Mutils.h, src/dgCMatrix.c: Define and use the Alloca macro
104              (like Calloc but calling alloca)
105    
106    2007-07-05  Martin Maechler  <maechler@stat.math.ethz.ch>
107    
108            * R/sparseMatrix.R (printSpMatrix): renamed from prSpMatrix()
109            and extended with more sophisticated 'col.names' option.
110            * NAMESPACE: export  printSparseMatrix()
111            * man/printSpMatrix.Rd: document, incl. examples
112    
113    2007-07-04 16:21  Douglas Bates <bates@stat.wisc.edu>
114    
115            * [r4543] src/cs_utils.c, src/cs_utils.h, src/dgCMatrix.c,
116              src/dtCMatrix.c, src/sparseQR.c: CSP typedef for *cs and macro
117              AS_CSP. API change - pass the empty structure to Matrix_as_cs.
118    
119    2007-07-04  Martin Maechler  <maechler@stat.math.ethz.ch>
120    
121            * DESCRIPTION (Version): 0.99875-4
122    
123            * tests/Class+Meth.R (tstMatrixClass): add dimnames, and hence test
124            some dimnames perservation.
125    
126            * R/dsTMatrix.R (t-method): keep dimnames
127            * R/dtTMatrix.R:  ditto
128    
129            * R/sparseMatrix.R (prSpMatrix): print colnames when non-trivial
130            and ncol(.) < 10
131    
132            * src/cs_utils.c: drop check_class() and use Matrix_check_class()
133            from Mutils.h
134    
135            * src/lgCMatrix.c ([ln]csc_to_matrix): no longer lose dimnames,
136            e.g. in as(<ngCMatrix>, "matrix")
137    
138    2007-07-01 13:27  Douglas Bates <bates@stat.wisc.edu>
139    
140            * [r4529] .: Create a branch for the API changes from the 0.99875
141              series to the 0.999375 series
142            * [r4530] DESCRIPTION, inst/include/Matrix.h,
143              inst/include/Matrix_stubs.c, src/CHMfactor.c, src/Csparse.c,
144              src/Mutils.h, src/Tsparse.c, src/chm_common.c, src/chm_common.h,
145              src/dense.c, src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c,
146              src/t_gCMatrix_colSums.c: API change - pass the empty structure to the
147              as_cholmod_x functions
148    
149    2007-06-30 09:05  Martin Maechler <maechler@stat.math.ethz.ch>
150    
151            * [r4527] trunk/Matrix/DESCRIPTION, trunk/Matrix/NAMESPACE,
152              trunk/Matrix/inst/doc/Comparisons.Rnw: add session- and hardware-info
153              to Comparisons
154    
155    >>>>>>> .merge-right.r4561
156    2007-06-29  Martin Maechler  <maechler@stat.math.ethz.ch>
157    
158            * DESCRIPTION (Version): 0.99875-3 ready to be released.
159    
160            * R/sparseMatrix.R (spMatrix): make spMatrix(3,4) working
161    
162            * R/AllGeneric.R: set "Math" (and "Math2") group generics in a way
163            that should also work in a future version of R.
164    
165    2007-06-21  Martin Maechler  <maechler@stat.math.ethz.ch>
166    
167            * NAMESPACE, R/AllClass.R: "xsparseVector" class union.
168    
169            * R/sparseVector.R: more *sparseVector coercions, notably for
170            non - double ones.
171    
172    2007-06-19  Martin Maechler  <maechler@stat.math.ethz.ch>
173    
174            * R/colSums.R: new file for all (col|row)(Sums|Means) methods,
175              notably the new ones building on the new .Call(.)s:
176    
177            * src/dgCMatrix.c (DEF_gCMatrix_COLSUMS): use to define
178            all 4 of [dlin]gCMatrix_colSums().
179    
180    2007-06-18 16:12  Douglas Bates <bates@stat.wisc.edu>
181    
182            * [r4472] src/Syms.h, src/init.c: Added Matrix_lengthSym
183            * [r4473] src/dgCMatrix.c: Modified dgCMatrix_colSums for sparseVector
184              result
185    
186    2007-06-16  Martin Maechler  <maechler@stat.math.ethz.ch>
187    
188            * R/kronecker.R: fix typo (could lead to inf.recursion)
189            * test/simple.R: testing that
190    
191            * R/sparseMatrix.R (prSpMatrix): change to be used as print()
192            method as well (which can have arguments, show() can't).
193    
194    2007-06-16 15:52  Douglas Bates <bates@stat.wisc.edu>
195    
196            * [r4466] R/dgCMatrix.R, src/dgCMatrix.c, src/dgCMatrix.h, src/init.c:
197              added dgCMatrix_colSums for [col,row][Sums,Means]
198    
199    2007-06-15 23:15  Douglas Bates <bates@stat.wisc.edu>
200    
201            * [r4460] R/sparseMatrix.R, man/dgCMatrix-class.Rd, src/dgCMatrix.c,
202              src/dgCMatrix.h, src/init.c: added lm.fit.sparse (unexported),
203              coercion of "factor" to "dgCMatrix" and dgCMatrix_cholsol
204            * [r4461] R/AllClass.R, man/sparseMatrix-class.Rd: draft "indicators"
205              class
206            * [r4463] R/sparseMatrix.R, man/dgCMatrix-class.Rd,
207              man/sparseMatrix-class.Rd: Don't need an "indicators" class - use the
208              row names to store the levels - duh!  Added an example.
209    
210    2007-06-14  Martin Maechler  <maechler@stat.math.ethz.ch>
211    
212            * src/Csparse.c (Csparse_validate): check for *repeated* entries
213            thanks to example from Christian Buchta; with a test here:
214            * tests/simple.R:
215    
216    2007-06-07  Martin Maechler  <maechler@stat.math.ethz.ch>
217    
218            * R/Auxiliaries.R (callGeneric): another fix, needed for some cases
219            of colSums(*, sparseResult = TRUE)
220    
221    2007-06-06  Martin Maechler  <maechler@stat.math.ethz.ch>
222    
223            * R/lsparseMatrix.R, R/ldenseMatrix.R (all, any): change default to
224            'na.rm = FALSE' as "everywhere" else in R.
225    
226    2007-06-05 Douglas Bates <bates@stat.wisc.edu>
227    
228            * [r4421] src/CSparse_install.sh: Modify for new organization of
229              CSparse package
230            * [r4425] src/UFsparse_download.sh: Update to version 3.0.0 of
231              SuiteSparse
232            * [r4426] src/Makefile: add ./UFconfig to the include path for
233              compilation
234            * [r4427] src/cs.[ch]: update to CSparse version 2.2.0
235            * [r4428] inst/doc/UFsparse/* src/{AMD,CHOLMOD,COLAMD}/*
236              src/UFconfig/UFconfig.h: Update to version 3.0.0 of SuiteSparse
237    
238    2007-06-05  Martin Maechler  <maechler@stat.math.ethz.ch>
239    
240            * R/Auxiliaries.R (emptyColnames): + argument msg.if.not.empty, used in
241            * R/sparseMatrix.R (prSpMatrix): now gives a message about
242            suppressed column names.
243    
244    2007-06-04 17:13  Douglas Bates <bates@stat.wisc.edu>
245    
246            * [r4418] src/Csparse.c, src/HBMM.c, src/Mutils.c, src/Mutils.h,
247              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dgCMatrix.c,
248              src/dgeMatrix.c, src/dpoMatrix.c, src/dpoMatrix.h, src/dppMatrix.c,
249              src/dppMatrix.h, src/dsCMatrix.c, src/dspMatrix.c, src/dspMatrix.h,
250              src/dsyMatrix.c, src/dsyMatrix.h, src/dtpMatrix.c, src/dtrMatrix.c:
251              Remove warnings after change to const char* CHAR
252    
253    2007-06-04 17:11  Douglas Bates <bates@stat.wisc.edu>
254    
255            * [r4417] inst/include/Matrix_stubs.c, inst/include/cholmod.h: Corrected
256              type of M_cholmod_ssmult
257    
258    2007-06-03 14:42  Douglas Bates <bates@stat.wisc.edu>
259    
260            * [r4412] inst/include/Matrix_stubs.c, inst/include/cholmod.h,
261              src/init.c: Yet another cholmod export - cholmod_ssmult
262    
263    2007-05-23  Martin Maechler  <maechler@stat.math.ethz.ch>
264    
265            * NAMESPACE: exported drop0(), since
266            * man/drop0.Rd: I have seen several cases, I really wanted to use
267            it, so our users may want too.
268    
269    2007-05-22  Martin Maechler  <maechler@stat.math.ethz.ch>
270    
271            * man/colSums.Rd: separately document colSums() etc, since these
272            have the extra argument 'sparseResult'.
273    
274    2007-05-21  Martin Maechler  <maechler@stat.math.ethz.ch>
275    
276            * R/sparseMatrix.R (spMatrix): utility (T)sparse Matrix constructor;
277            * man/spMatrix.Rd: docu., including examples
278    
279            * R/Auxiliaries.R (sp.colMeans): etc, using a patched callGeneric(),
280            in order to make colMeans() etc fast *and* correct.
281            * R/sparseVector.R (replSPvec): "[<-" functionality for
282            sparseVectors; tested in
283            * tests/simple.R:
284    
285    2007-05-19  Martin Maechler  <maechler@stat.math.ethz.ch>
286    
287            * R/sparseMatrix.R (print.sparseSummary): and summary() method for
288            (very) sparse Matrices; output similar to Matlab's print().
289    
290    2007-05-17  Douglas Bates  <bates@stat.wisc.edu>
291    
292            * src/HBMM.c (Matrix_writeMatrixMarket): Write 1-based, not
293            0-based, indices (Jose Quesada <quesada@gmail.com>).
294    
295    2007-05-16  Douglas Bates  <bates@stat.wisc.edu>
296    
297            * R/CHMfactor.R: Added solve methods for a CHMfactor object.
298    
299    2007-05-16  Martin Maechler  <maechler@stat.math.ethz.ch>
300    
301            * R/Auxiliaries.R (sparsapply): new utility, much faster than
302            tapply1() for large sparse matrices.
303    
304    2007-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
305    
306            * R/Matrix.R (dim<-): reshape now via sparseVector.
307    
308            * R/sparseVector.R: methods and function for
309            * R/AllClass.R: new "sparseVector" class and daughters.
310            * NAMESPACE: export new classes
311    
312    2007-05-14  Martin Maechler  <maechler@stat.math.ethz.ch>
313    
314            * DESCRIPTION (Version): 0.99875-1
315            * src/Makefile.win: also remove Lapack code from here (cf. 04-25).
316    
317    2007-05-11  Martin Maechler  <maechler@stat.math.ethz.ch>
318    
319            * R/Tsparse.R ([, Tsparse): fix last case: *duplicated*, symmetric
320            indexing
321            * tests/indexing.R: test set for that.
322    
323    2007-05-08  Martin Maechler  <maechler@stat.math.ethz.ch>
324    
325            * R/Tsparse.R (replTmat): fix the case of *duplicated* index
326            entries.
327            * tests/indexing.R(out): add regression test for it
328    
329    2007-04-30  Martin Maechler  <maechler@stat.math.ethz.ch>
330    
331            * R/(l(dense|sparse))?Matrix.R (!): use 'x', not 'e1' as argument
332            name for "!" method definitions.
333    
334    2007-04-26  Martin Maechler  <maechler@stat.math.ethz.ch>
335    
336            * R/Tsparse.R (intI): new utility, used for "[" :
337                    Cleanup up there, and fixes for duplicated indices - more TODO!
338    
339            * tests/indexing.R(out): more tests
340    
341    2007-04-25  Douglas Bates  <bates@stat.wisc.edu>
342    
343            * DESCRIPTION,src/Makefile: require R>= 2.5.0 and remove Lapack
344            code that is now part of the R Lapack library.
345    
346            * src/init.c,inst/include/{Matrix_stubs.c,cholmod.h}:export
347            cholmod_factorize_p (used in lme4 for GLMMs and NLMMs).
348    
349    2007-04-21  Martin Maechler  <maechler@stat.math.ethz.ch>
350    
351            * R/Matrix.R (image): method for all Matrices, not just sparse ones.
352    
353    2007-04-17  Martin Maechler  <maechler@stat.math.ethz.ch>
354    
355            * R/Auxiliaries.R (tapply1): unname(.) -> colSums() etc don't end
356            up with extraneous names '0'...'<n-1>'
357    
358    2007-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
359    
360            * R/dgTMatrix.R (mat2dgT): care about NAs
361    
362    2007-04-11  Martin Maechler  <maechler@stat.math.ethz.ch>
363    
364            * R/kronecker.R: triangularity preserving methods
365    
366    2007-03-27  Martin Maechler  <maechler@stat.math.ethz.ch>
367    
368            * R/kronecker.R: new file collecting kronecker() methods in one
369                    place.  Goal: become much faster!
370    
371    2007-03-23  Martin Maechler  <maechler@stat.math.ethz.ch>
372    
373            * src/dtCMatrix.c (dtCMatrix_solve): use the new code from Kasper
374            Kristensen based cs_spsolve() instead of _lsolve & _usolve which
375            can be much faster.
376    
377            * tests/matprod.R: add regression tests for these (upper & lower).
378    
379    2007-03-19  Martin Maechler  <maechler@stat.math.ethz.ch>
380    
381            * R/Matrix.R (diff): method for our Matrices.
382    
383            * R/sparseMatrix.R (isDiagonal): check dim()!
384    
385    2007-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
386    
387            * R/Matrix.R (dim<-): new method for "reshape()" built on a
388            proposal from Tamas Papp.
389    
390    2007-03-16  Martin Maechler  <maechler@stat.math.ethz.ch>
391    
392            * R/AllGeneric.R: remove all  if(!isGeneric(.))  clauses
393    
394            * R/zzz.R (.onLoad, .onUnload): do *not* leave bind_activation(TRUE);
395            rather define and export  cBind() and rBind() only.
396            --> useRs *must* change code that used to have cbind()/rbind() !!
397    
398            * R/bind.R: change tests from cbind() to cBind() and similarly to rBind()
399            * R/bind.Rout.save: ditto
400    
401    2007-02-16  Douglas Bates  <bates@r-project.org>
402    
403            * DESCRIPTION (Date, Version): 0.9975-11 with new date
404            * src/dgCMatrix.c (R_to_CMatrix, compressed_to_TMatrix): remove
405            const modifier on declaration of the array 'valid'
406    
407    2007-02-12  Douglas Bates  <bates@stat.wisc.edu>
408    
409            * R/CHMfactor.R: Add image method (coercion to sparseMatrix).
410    
411  2007-02-05  Martin Maechler  <maechler@stat.math.ethz.ch>  2007-02-05  Martin Maechler  <maechler@stat.math.ethz.ch>
412    
413          * DESCRIPTION (Date, Version): 0.9975-10 with new date.          * DESCRIPTION (Date, Version): 0.9975-10 with new date.

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