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revision 1827, Wed Apr 25 22:22:41 2007 UTC revision 2024, Thu Aug 2 07:22:44 2007 UTC
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1    2007-08-02  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * DESCRIPTION (Date): set ready for release
4    
5    2007-08-01 15:44  Douglas Bates <bates@stat.wisc.edu>
6    
7            * [r4686] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
8              src/chm_common.c, src/chm_common.h: Change API for
9              numeric_as_chm_dense and N_AS_CHM_DN
10    
11    2007-08-01  Martin Maechler  <maechler@stat.math.ethz.ch>
12    
13            * src/dtrMatrix.c (dtrMatrix_matrix_mm): fix dimensionality check (!)
14            * tests/matprod.R: regr.test for it
15    
16    2007-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
17    
18            * R/dMatrix.R: fix from Brian for   Math2(., digits = "missing")
19            * tests/group-methods.R: and regression-test it
20    
21    2007-07-19 19:45  Douglas Bates <bates@stat.wisc.edu>
22    
23            * [r4642] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
24              inst/include/cholmod.h, src/chm_common.c, src/init.c: Export
25              triplet_to_sparse, documentation, use typedefs
26    
27    2007-07-18  Martin Maechler  <maechler@stat.math.ethz.ch>
28    
29            * man/dpoMatrix-class.Rd: added 'corMatrix' example
30    
31            * src/dsyMatrix.[ch] (dsyMatrix_as_matrix): new 'keep_dimnames' arg
32            * src/dtrMatrix.[ch] (dtrMatrix_as_matrix): ditto
33            * src/init.c, R/dsyMatrix.R, R/dtrMatrix.R, R/lgTMatrix.R: ditto
34    
35            * R/lsparseMatrix.R: bug fix in "all" method
36            * R/Ops.R (.do.Logic.lsparse): "|" bug in borderline case
37    
38            * R/dsyMatrix.R (coerce->dsTMatrix): (i,j) slots should *not* have names
39            * R/ngTMatrix.R (coerce->ngTMatrix): ditto;
40                    + matrix |-> nMatrix coercion
41            * R/pMatrix.R: + setAs()  to dMatrix and from nMatrix
42            * man/pMatrix-class.Rd: ditto
43    
44            * R/Matrix.R (Summary): method for non-dMatrix
45    
46            * tests/Class+Meth.R (extraValid): new check about "dirty" slots
47            * tests/Class+Meth.R (tstMatrixClass): test norm(.);
48                    test all Summary methods.
49    
50    2007-07-16  Martin Maechler  <maechler@stat.math.ethz.ch>
51    
52            * R/dgeMatrix.R (norm, rcond): methods for 'matrix'
53    
54    2007-07-14  Martin Maechler  <maechler@stat.math.ethz.ch>
55    
56            * R/sparseMatrix.R (norm): simple methods for sparseMatrix
57    
58            * R/pMatrix.R (t?crossprod): methods for pMatrix
59    
60    2007-07-10  Douglas Bates  <bates@stat.wisc.edu>
61    
62            * src/dgeMatrix.c (dgeMatrix_colsums): Get the logic straight.
63    
64    2007-07-09 20:45  Douglas Bates <bates@stat.wisc.edu>
65    
66            * [r4579] src/dgeMatrix.c: Untangle horrible code in dgeMatrix_colsums
67              trying to fix a subtle bug - which has been somewhere else.
68    
69    2007-07-09 19:43  Martin Maechler <maechler@stat.math.ethz.ch>
70    
71            * [r4578] src/dgeMatrix.c: "cleaned" dgeMatrix_colsums() - but did not
72              solve the bug
73    
74    2007-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
75    
76            * src/dgCMatrix.c (compressed_to_TMatrix):
77    
78    2007-07-07  Martin Maechler  <maechler@stat.math.ethz.ch>
79    
80            * src/Csparse.c (Rsparse_validate): new, to have some validity
81            checking for RsparseMatrix
82            * src/dgCMatrix.c (xRMatrix_validate): ditto
83            * src/dtCMatrix.c (tRMatrix_validate): ditto
84    
85    2007-07-07  Douglas Bates <bates@stat.wisc.edu>
86    
87            * [r4567] R/AllClass.R: Slots already in RsparseMatrix were redefined in
88              lgRMatrix
89            * [r4568] DESCRIPTION: Prepare for bug-fix release
90            * [r4570] src/CHOLMOD/Check/cholmod_write.c: Include cholmod_matrixops.h
91              for declaration of cholmod_symmetry
92    
93    2007-07-06  Martin Maechler  <maechler@stat.math.ethz.ch>
94    
95            * DESCRIPTION (Version): 0.999375 merged into the trunk; ready for
96            release.
97    
98    2007-07-06 14:11  Douglas Bates <bates@stat.wisc.edu>
99    
100            * [r4559] src/iohb.c, src/iohb.h: Remove Harwell-Boeing input/output
101              functions - no longer used
102            * [r4560] src/HBMM.c, src/Mutils.c, src/dgTMatrix.c, src/dgeMatrix.c,
103              src/dspMatrix.c, src/dsyMatrix.c, src/dtCMatrix.c,
104              src/factorizations.c, src/sparseQR.c: Replace most calls to Calloc by
105              Alloca
106    
107    2007-07-06 13:14  Martin Maechler <maechler@stat.math.ethz.ch>
108    
109            * [r4558] inst/doc/Comparisons.Rnw, src/CHMfactor.c, src/Csparse.c,
110              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dense.c,
111              src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c, src/sparseQR.c,
112              src/t_gCMatrix_colSums.c: more R_CheckStack()s
113    
114    2007-07-05 18:12  Douglas Bates <bates@stat.wisc.edu>
115    
116            * [r4550] inst/include/Matrix.h: Add the macro N_AS_CHM_DN to "alloca"
117              the required amount of memory then call M_numeric_as_chm_dense.
118            * [r4556] src/Mutils.h, src/dgCMatrix.c: Define and use the Alloca macro
119              (like Calloc but calling alloca)
120    
121    2007-07-05  Martin Maechler  <maechler@stat.math.ethz.ch>
122    
123            * R/sparseMatrix.R (printSpMatrix): renamed from prSpMatrix()
124            and extended with more sophisticated 'col.names' option.
125            * NAMESPACE: export  printSparseMatrix()
126            * man/printSpMatrix.Rd: document, incl. examples
127    
128    2007-07-04 16:21  Douglas Bates <bates@stat.wisc.edu>
129    
130            * [r4543] src/cs_utils.c, src/cs_utils.h, src/dgCMatrix.c,
131              src/dtCMatrix.c, src/sparseQR.c: CSP typedef for *cs and macro
132              AS_CSP. API change - pass the empty structure to Matrix_as_cs.
133    
134    2007-07-04  Martin Maechler  <maechler@stat.math.ethz.ch>
135    
136            * DESCRIPTION (Version): 0.99875-4
137    
138            * tests/Class+Meth.R (tstMatrixClass): add dimnames, and hence test
139            some dimnames perservation.
140    
141            * R/dsTMatrix.R (t-method): keep dimnames
142            * R/dtTMatrix.R:  ditto
143    
144            * R/sparseMatrix.R (prSpMatrix): print colnames when non-trivial
145            and ncol(.) < 10
146    
147            * src/cs_utils.c: drop check_class() and use Matrix_check_class()
148            from Mutils.h
149    
150            * src/lgCMatrix.c ([ln]csc_to_matrix): no longer lose dimnames,
151            e.g. in as(<ngCMatrix>, "matrix")
152    
153    2007-07-01 13:27  Douglas Bates <bates@stat.wisc.edu>
154    
155            * [r4529] .: Create a branch for the API changes from the 0.99875
156              series to the 0.999375 series
157            * [r4530] DESCRIPTION, inst/include/Matrix.h,
158              inst/include/Matrix_stubs.c, src/CHMfactor.c, src/Csparse.c,
159              src/Mutils.h, src/Tsparse.c, src/chm_common.c, src/chm_common.h,
160              src/dense.c, src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c,
161              src/t_gCMatrix_colSums.c: API change - pass the empty structure to the
162              as_cholmod_x functions
163    
164    2007-06-30 09:05  Martin Maechler <maechler@stat.math.ethz.ch>
165    
166            * [r4527] trunk/Matrix/DESCRIPTION, trunk/Matrix/NAMESPACE,
167              trunk/Matrix/inst/doc/Comparisons.Rnw: add session- and hardware-info
168              to Comparisons
169    
170    >>>>>>> .merge-right.r4561
171    2007-06-29  Martin Maechler  <maechler@stat.math.ethz.ch>
172    
173            * DESCRIPTION (Version): 0.99875-3 ready to be released.
174    
175            * R/sparseMatrix.R (spMatrix): make spMatrix(3,4) working
176    
177            * R/AllGeneric.R: set "Math" (and "Math2") group generics in a way
178            that should also work in a future version of R.
179    
180    2007-06-21  Martin Maechler  <maechler@stat.math.ethz.ch>
181    
182            * NAMESPACE, R/AllClass.R: "xsparseVector" class union.
183    
184            * R/sparseVector.R: more *sparseVector coercions, notably for
185            non - double ones.
186    
187    2007-06-19  Martin Maechler  <maechler@stat.math.ethz.ch>
188    
189            * R/colSums.R: new file for all (col|row)(Sums|Means) methods,
190              notably the new ones building on the new .Call(.)s:
191    
192            * src/dgCMatrix.c (DEF_gCMatrix_COLSUMS): use to define
193            all 4 of [dlin]gCMatrix_colSums().
194    
195    2007-06-18 16:12  Douglas Bates <bates@stat.wisc.edu>
196    
197            * [r4472] src/Syms.h, src/init.c: Added Matrix_lengthSym
198            * [r4473] src/dgCMatrix.c: Modified dgCMatrix_colSums for sparseVector
199              result
200    
201    2007-06-16  Martin Maechler  <maechler@stat.math.ethz.ch>
202    
203            * R/kronecker.R: fix typo (could lead to inf.recursion)
204            * test/simple.R: testing that
205    
206            * R/sparseMatrix.R (prSpMatrix): change to be used as print()
207            method as well (which can have arguments, show() can't).
208    
209    2007-06-16 15:52  Douglas Bates <bates@stat.wisc.edu>
210    
211            * [r4466] R/dgCMatrix.R, src/dgCMatrix.c, src/dgCMatrix.h, src/init.c:
212              added dgCMatrix_colSums for [col,row][Sums,Means]
213    
214    2007-06-15 23:15  Douglas Bates <bates@stat.wisc.edu>
215    
216            * [r4460] R/sparseMatrix.R, man/dgCMatrix-class.Rd, src/dgCMatrix.c,
217              src/dgCMatrix.h, src/init.c: added lm.fit.sparse (unexported),
218              coercion of "factor" to "dgCMatrix" and dgCMatrix_cholsol
219            * [r4461] R/AllClass.R, man/sparseMatrix-class.Rd: draft "indicators"
220              class
221            * [r4463] R/sparseMatrix.R, man/dgCMatrix-class.Rd,
222              man/sparseMatrix-class.Rd: Don't need an "indicators" class - use the
223              row names to store the levels - duh!  Added an example.
224    
225    2007-06-14  Martin Maechler  <maechler@stat.math.ethz.ch>
226    
227            * src/Csparse.c (Csparse_validate): check for *repeated* entries
228            thanks to example from Christian Buchta; with a test here:
229            * tests/simple.R:
230    
231    2007-06-07  Martin Maechler  <maechler@stat.math.ethz.ch>
232    
233            * R/Auxiliaries.R (callGeneric): another fix, needed for some cases
234            of colSums(*, sparseResult = TRUE)
235    
236    2007-06-06  Martin Maechler  <maechler@stat.math.ethz.ch>
237    
238            * R/lsparseMatrix.R, R/ldenseMatrix.R (all, any): change default to
239            'na.rm = FALSE' as "everywhere" else in R.
240    
241    2007-06-05 Douglas Bates <bates@stat.wisc.edu>
242    
243            * [r4421] src/CSparse_install.sh: Modify for new organization of
244              CSparse package
245            * [r4425] src/UFsparse_download.sh: Update to version 3.0.0 of
246              SuiteSparse
247            * [r4426] src/Makefile: add ./UFconfig to the include path for
248              compilation
249            * [r4427] src/cs.[ch]: update to CSparse version 2.2.0
250            * [r4428] inst/doc/UFsparse/* src/{AMD,CHOLMOD,COLAMD}/*
251              src/UFconfig/UFconfig.h: Update to version 3.0.0 of SuiteSparse
252    
253    2007-06-05  Martin Maechler  <maechler@stat.math.ethz.ch>
254    
255            * R/Auxiliaries.R (emptyColnames): + argument msg.if.not.empty, used in
256            * R/sparseMatrix.R (prSpMatrix): now gives a message about
257            suppressed column names.
258    
259    2007-06-04 17:13  Douglas Bates <bates@stat.wisc.edu>
260    
261            * [r4418] src/Csparse.c, src/HBMM.c, src/Mutils.c, src/Mutils.h,
262              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dgCMatrix.c,
263              src/dgeMatrix.c, src/dpoMatrix.c, src/dpoMatrix.h, src/dppMatrix.c,
264              src/dppMatrix.h, src/dsCMatrix.c, src/dspMatrix.c, src/dspMatrix.h,
265              src/dsyMatrix.c, src/dsyMatrix.h, src/dtpMatrix.c, src/dtrMatrix.c:
266              Remove warnings after change to const char* CHAR
267    
268    2007-06-04 17:11  Douglas Bates <bates@stat.wisc.edu>
269    
270            * [r4417] inst/include/Matrix_stubs.c, inst/include/cholmod.h: Corrected
271              type of M_cholmod_ssmult
272    
273    2007-06-03 14:42  Douglas Bates <bates@stat.wisc.edu>
274    
275            * [r4412] inst/include/Matrix_stubs.c, inst/include/cholmod.h,
276              src/init.c: Yet another cholmod export - cholmod_ssmult
277    
278    2007-05-23  Martin Maechler  <maechler@stat.math.ethz.ch>
279    
280            * NAMESPACE: exported drop0(), since
281            * man/drop0.Rd: I have seen several cases, I really wanted to use
282            it, so our users may want too.
283    
284    2007-05-22  Martin Maechler  <maechler@stat.math.ethz.ch>
285    
286            * man/colSums.Rd: separately document colSums() etc, since these
287            have the extra argument 'sparseResult'.
288    
289    2007-05-21  Martin Maechler  <maechler@stat.math.ethz.ch>
290    
291            * R/sparseMatrix.R (spMatrix): utility (T)sparse Matrix constructor;
292            * man/spMatrix.Rd: docu., including examples
293    
294            * R/Auxiliaries.R (sp.colMeans): etc, using a patched callGeneric(),
295            in order to make colMeans() etc fast *and* correct.
296            * R/sparseVector.R (replSPvec): "[<-" functionality for
297            sparseVectors; tested in
298            * tests/simple.R:
299    
300    2007-05-19  Martin Maechler  <maechler@stat.math.ethz.ch>
301    
302            * R/sparseMatrix.R (print.sparseSummary): and summary() method for
303            (very) sparse Matrices; output similar to Matlab's print().
304    
305    2007-05-17  Douglas Bates  <bates@stat.wisc.edu>
306    
307            * src/HBMM.c (Matrix_writeMatrixMarket): Write 1-based, not
308            0-based, indices (Jose Quesada <quesada@gmail.com>).
309    
310    2007-05-16  Douglas Bates  <bates@stat.wisc.edu>
311    
312            * R/CHMfactor.R: Added solve methods for a CHMfactor object.
313    
314    2007-05-16  Martin Maechler  <maechler@stat.math.ethz.ch>
315    
316            * R/Auxiliaries.R (sparsapply): new utility, much faster than
317            tapply1() for large sparse matrices.
318    
319    2007-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
320    
321            * R/Matrix.R (dim<-): reshape now via sparseVector.
322    
323            * R/sparseVector.R: methods and function for
324            * R/AllClass.R: new "sparseVector" class and daughters.
325            * NAMESPACE: export new classes
326    
327    2007-05-14  Martin Maechler  <maechler@stat.math.ethz.ch>
328    
329            * DESCRIPTION (Version): 0.99875-1
330            * src/Makefile.win: also remove Lapack code from here (cf. 04-25).
331    
332    2007-05-11  Martin Maechler  <maechler@stat.math.ethz.ch>
333    
334            * R/Tsparse.R ([, Tsparse): fix last case: *duplicated*, symmetric
335            indexing
336            * tests/indexing.R: test set for that.
337    
338    2007-05-08  Martin Maechler  <maechler@stat.math.ethz.ch>
339    
340            * R/Tsparse.R (replTmat): fix the case of *duplicated* index
341            entries.
342            * tests/indexing.R(out): add regression test for it
343    
344    2007-04-30  Martin Maechler  <maechler@stat.math.ethz.ch>
345    
346            * R/(l(dense|sparse))?Matrix.R (!): use 'x', not 'e1' as argument
347            name for "!" method definitions.
348    
349    2007-04-26  Martin Maechler  <maechler@stat.math.ethz.ch>
350    
351            * R/Tsparse.R (intI): new utility, used for "[" :
352                    Cleanup up there, and fixes for duplicated indices - more TODO!
353    
354            * tests/indexing.R(out): more tests
355    
356  2007-04-25  Douglas Bates  <bates@stat.wisc.edu>  2007-04-25  Douglas Bates  <bates@stat.wisc.edu>
357    
358          * DESCRIPTION,src/Makefile: require R>= 2.5.0 and remove Lapack          * DESCRIPTION,src/Makefile: require R>= 2.5.0 and remove Lapack
# Line 6  Line 361 
361          * src/init.c,inst/include/{Matrix_stubs.c,cholmod.h}:export          * src/init.c,inst/include/{Matrix_stubs.c,cholmod.h}:export
362          cholmod_factorize_p (used in lme4 for GLMMs and NLMMs).          cholmod_factorize_p (used in lme4 for GLMMs and NLMMs).
363    
364    2007-04-21  Martin Maechler  <maechler@stat.math.ethz.ch>
365    
366            * R/Matrix.R (image): method for all Matrices, not just sparse ones.
367    
368    2007-04-17  Martin Maechler  <maechler@stat.math.ethz.ch>
369    
370            * R/Auxiliaries.R (tapply1): unname(.) -> colSums() etc don't end
371            up with extraneous names '0'...'<n-1>'
372    
373  2007-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>  2007-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
374    
375          * R/dgTMatrix.R (mat2dgT): care about NAs          * R/dgTMatrix.R (mat2dgT): care about NAs

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