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revision 1827, Wed Apr 25 22:22:41 2007 UTC revision 2069, Sun Sep 23 17:35:17 2007 UTC
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1    2007-09-23 17:32  Douglas Bates <bates@stat.wisc.edu>
2    
3            * [r4778] R/AllGeneric.R: Check R version before defining generics for
4              primitives
5    
6    2007-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
7    
8            * R/Matrix.R ([<-): add (Matrix,missing,ANY,Matrix) etc
9            * tests/indexing.R: add new regression for the above cases.
10    
11    2007-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
12    
13            * src/Mutils.h (__sun): clause for alloca.h on Solaris
14    
15    2007-08-16  Martin Maechler  <maechler@stat.math.ethz.ch>
16    
17            * DESCRIPTION (Date, Version): 0.999375-2
18    
19    2007-08-15  Martin Maechler  <maechler@stat.math.ethz.ch>
20    
21            * R/HBMM.R (readMM): make work for pattern matrices as well
22    
23    2007-08-14 13:07  Douglas Bates <bates@stat.wisc.edu>
24    
25            * [r4730] src/Mutils.h: declare alloca
26            * [r4734] NAMESPACE, R/AllGeneric.R, R/Csparse.R, R/HBMM.R, R/Tsparse.R,
27              R/dgCMatrix.R, R/dgTMatrix.R, R/dsCMatrix.R, R/dsTMatrix.R,
28              man/externalFormats.Rd, src/Csparse.c, src/Csparse.h, src/DEPS.mkf,
29              src/HBMM.c, src/HBMM.h, src/Mutils.h, src/SOURCES_C.mkf, src/init.c,
30              src/mmio.c, src/mmio.h: Remove deprecated function writeHB and its
31              methods; switch writeMM to use CHOLMOD code; repair readMM
32    
33    2007-08-14  Martin Maechler  <maechler@stat.math.ethz.ch>
34    
35            * R/nearPD.R, man/nearPD.Rd (nearPD): new function built on Jens
36            Oehlschlaegel's ... result type still to be discussed!
37    
38    2007-08-10  Martin Maechler  <maechler@stat.math.ethz.ch>
39    
40            * man/image-methods.Rd: new, combining all image() methods
41    
42    2007-08-09  Martin Maechler  <maechler@stat.math.ethz.ch>
43    
44            * R/dgCMatrix.R: define qr() and lu() methods for "sparseMatrix"
45            to work via dgC...
46    
47            * R/Matrix.R (Matrix): special treatment for "table" (S3)
48    
49    2007-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
50    
51            * R/dgTMatrix.R (image): change defaults to
52                    aspect = "iso", colorkey = FALSE
53    
54    2007-08-06  Martin Maechler  <maechler@stat.math.ethz.ch>
55    
56            * src/dsyMatrix.c (dsyMatrix_matrix_mm): 'b' might be matrix;
57            must copy its *expanded* x slot before LAPACK call.
58    
59            * tests/matprod.R: test the last days' changes.
60    
61    2007-08-06 16:43  Douglas Bates <bates@stat.wisc.edu>
62    
63            * [r4712] inst/include/Matrix_stubs.c: Change R_cholmod_printf in stubs
64              as well as in sources
65            * [r4713] src/dsyMatrix.c: Duplicate the contents of the RHS before
66              Lapack call
67    
68    2007-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
69    
70            * R/Matrix.R (%*%, crossprod, tcrossprod): add method for
71                    ("Matrix", "matrix") which is needed in some cases.
72            Ditto for solve().
73    
74            * R/colSums.R (.as.dge.Fun): need ddenseMatrix methods to avoid
75            infinite recursion in dispatch for some cases.
76    
77    2007-08-02 08:48  Martin Maechler <maechler@stat.math.ethz.ch>
78    
79            * [r4693] src/chm_common.c: R_cholmod_printf() instead of Rprintf() just
80              so pointers match
81    
82    2007-08-02  Martin Maechler  <maechler@stat.math.ethz.ch>
83    
84            * DESCRIPTION (Date): set ready for release -- 0.999375-1
85    
86    2007-08-01 15:44  Douglas Bates <bates@stat.wisc.edu>
87    
88            * [r4686] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
89              src/chm_common.c, src/chm_common.h: Change API for
90              numeric_as_chm_dense and N_AS_CHM_DN
91    
92    2007-08-01  Martin Maechler  <maechler@stat.math.ethz.ch>
93    
94            * src/dtrMatrix.c (dtrMatrix_matrix_mm): fix dimensionality check (!)
95            * tests/matprod.R: regr.test for it
96    
97    2007-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
98    
99            * R/dMatrix.R: fix from Brian for   Math2(., digits = "missing")
100            * tests/group-methods.R: and regression-test it
101    
102    2007-07-19 19:45  Douglas Bates <bates@stat.wisc.edu>
103    
104            * [r4642] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
105              inst/include/cholmod.h, src/chm_common.c, src/init.c: Export
106              triplet_to_sparse, documentation, use typedefs
107    
108    2007-07-18  Martin Maechler  <maechler@stat.math.ethz.ch>
109    
110            * man/dpoMatrix-class.Rd: added 'corMatrix' example
111    
112            * src/dsyMatrix.[ch] (dsyMatrix_as_matrix): new 'keep_dimnames' arg
113            * src/dtrMatrix.[ch] (dtrMatrix_as_matrix): ditto
114            * src/init.c, R/dsyMatrix.R, R/dtrMatrix.R, R/lgTMatrix.R: ditto
115    
116            * R/lsparseMatrix.R: bug fix in "all" method
117            * R/Ops.R (.do.Logic.lsparse): "|" bug in borderline case
118    
119            * R/dsyMatrix.R (coerce->dsTMatrix): (i,j) slots should *not* have names
120            * R/ngTMatrix.R (coerce->ngTMatrix): ditto;
121                    + matrix |-> nMatrix coercion
122            * R/pMatrix.R: + setAs()  to dMatrix and from nMatrix
123            * man/pMatrix-class.Rd: ditto
124    
125            * R/Matrix.R (Summary): method for non-dMatrix
126    
127            * tests/Class+Meth.R (extraValid): new check about "dirty" slots
128            * tests/Class+Meth.R (tstMatrixClass): test norm(.);
129                    test all Summary methods.
130    
131    2007-07-16  Martin Maechler  <maechler@stat.math.ethz.ch>
132    
133            * R/dgeMatrix.R (norm, rcond): methods for 'matrix'
134    
135    2007-07-14  Martin Maechler  <maechler@stat.math.ethz.ch>
136    
137            * R/sparseMatrix.R (norm): simple methods for sparseMatrix
138    
139            * R/pMatrix.R (t?crossprod): methods for pMatrix
140    
141    2007-07-10  Douglas Bates  <bates@stat.wisc.edu>
142    
143            * src/dgeMatrix.c (dgeMatrix_colsums): Get the logic straight.
144    
145    2007-07-09 20:45  Douglas Bates <bates@stat.wisc.edu>
146    
147            * [r4579] src/dgeMatrix.c: Untangle horrible code in dgeMatrix_colsums
148              trying to fix a subtle bug - which has been somewhere else.
149    
150    2007-07-09 19:43  Martin Maechler <maechler@stat.math.ethz.ch>
151    
152            * [r4578] src/dgeMatrix.c: "cleaned" dgeMatrix_colsums() - but did not
153              solve the bug
154    
155    2007-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
156    
157            * src/dgCMatrix.c (compressed_to_TMatrix):
158    
159    2007-07-07  Martin Maechler  <maechler@stat.math.ethz.ch>
160    
161            * src/Csparse.c (Rsparse_validate): new, to have some validity
162            checking for RsparseMatrix
163            * src/dgCMatrix.c (xRMatrix_validate): ditto
164            * src/dtCMatrix.c (tRMatrix_validate): ditto
165    
166    2007-07-07  Douglas Bates <bates@stat.wisc.edu>
167    
168            * [r4567] R/AllClass.R: Slots already in RsparseMatrix were redefined in
169              lgRMatrix
170            * [r4568] DESCRIPTION: Prepare for bug-fix release
171            * [r4570] src/CHOLMOD/Check/cholmod_write.c: Include cholmod_matrixops.h
172              for declaration of cholmod_symmetry
173    
174    2007-07-06  Martin Maechler  <maechler@stat.math.ethz.ch>
175    
176            * DESCRIPTION (Version): 0.999375 merged into the trunk; ready for
177            release.
178    
179    2007-07-06 14:11  Douglas Bates <bates@stat.wisc.edu>
180    
181            * [r4559] src/iohb.c, src/iohb.h: Remove Harwell-Boeing input/output
182              functions - no longer used
183            * [r4560] src/HBMM.c, src/Mutils.c, src/dgTMatrix.c, src/dgeMatrix.c,
184              src/dspMatrix.c, src/dsyMatrix.c, src/dtCMatrix.c,
185              src/factorizations.c, src/sparseQR.c: Replace most calls to Calloc by
186              Alloca
187    
188    2007-07-06 13:14  Martin Maechler <maechler@stat.math.ethz.ch>
189    
190            * [r4558] inst/doc/Comparisons.Rnw, src/CHMfactor.c, src/Csparse.c,
191              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dense.c,
192              src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c, src/sparseQR.c,
193              src/t_gCMatrix_colSums.c: more R_CheckStack()s
194    
195    2007-07-05 18:12  Douglas Bates <bates@stat.wisc.edu>
196    
197            * [r4550] inst/include/Matrix.h: Add the macro N_AS_CHM_DN to "alloca"
198              the required amount of memory then call M_numeric_as_chm_dense.
199            * [r4556] src/Mutils.h, src/dgCMatrix.c: Define and use the Alloca macro
200              (like Calloc but calling alloca)
201    
202    2007-07-05  Martin Maechler  <maechler@stat.math.ethz.ch>
203    
204            * R/sparseMatrix.R (printSpMatrix): renamed from prSpMatrix()
205            and extended with more sophisticated 'col.names' option.
206            * NAMESPACE: export  printSparseMatrix()
207            * man/printSpMatrix.Rd: document, incl. examples
208    
209    2007-07-04 16:21  Douglas Bates <bates@stat.wisc.edu>
210    
211            * [r4543] src/cs_utils.c, src/cs_utils.h, src/dgCMatrix.c,
212              src/dtCMatrix.c, src/sparseQR.c: CSP typedef for *cs and macro
213              AS_CSP. API change - pass the empty structure to Matrix_as_cs.
214    
215    2007-07-04  Martin Maechler  <maechler@stat.math.ethz.ch>
216    
217            * DESCRIPTION (Version): 0.99875-4
218    
219            * tests/Class+Meth.R (tstMatrixClass): add dimnames, and hence test
220            some dimnames perservation.
221    
222            * R/dsTMatrix.R (t-method): keep dimnames
223            * R/dtTMatrix.R:  ditto
224    
225            * R/sparseMatrix.R (prSpMatrix): print colnames when non-trivial
226            and ncol(.) < 10
227    
228            * src/cs_utils.c: drop check_class() and use Matrix_check_class()
229            from Mutils.h
230    
231            * src/lgCMatrix.c ([ln]csc_to_matrix): no longer lose dimnames,
232            e.g. in as(<ngCMatrix>, "matrix")
233    
234    2007-07-01 13:27  Douglas Bates <bates@stat.wisc.edu>
235    
236            * [r4529] .: Create a branch for the API changes from the 0.99875
237              series to the 0.999375 series
238            * [r4530] DESCRIPTION, inst/include/Matrix.h,
239              inst/include/Matrix_stubs.c, src/CHMfactor.c, src/Csparse.c,
240              src/Mutils.h, src/Tsparse.c, src/chm_common.c, src/chm_common.h,
241              src/dense.c, src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c,
242              src/t_gCMatrix_colSums.c: API change - pass the empty structure to the
243              as_cholmod_x functions
244    
245    2007-06-30 09:05  Martin Maechler <maechler@stat.math.ethz.ch>
246    
247            * [r4527] trunk/Matrix/DESCRIPTION, trunk/Matrix/NAMESPACE,
248              trunk/Matrix/inst/doc/Comparisons.Rnw: add session- and hardware-info
249              to Comparisons
250    
251    >>>>>>> .merge-right.r4561
252    2007-06-29  Martin Maechler  <maechler@stat.math.ethz.ch>
253    
254            * DESCRIPTION (Version): 0.99875-3 ready to be released.
255    
256            * R/sparseMatrix.R (spMatrix): make spMatrix(3,4) working
257    
258            * R/AllGeneric.R: set "Math" (and "Math2") group generics in a way
259            that should also work in a future version of R.
260    
261    2007-06-21  Martin Maechler  <maechler@stat.math.ethz.ch>
262    
263            * NAMESPACE, R/AllClass.R: "xsparseVector" class union.
264    
265            * R/sparseVector.R: more *sparseVector coercions, notably for
266            non - double ones.
267    
268    2007-06-19  Martin Maechler  <maechler@stat.math.ethz.ch>
269    
270            * R/colSums.R: new file for all (col|row)(Sums|Means) methods,
271              notably the new ones building on the new .Call(.)s:
272    
273            * src/dgCMatrix.c (DEF_gCMatrix_COLSUMS): use to define
274            all 4 of [dlin]gCMatrix_colSums().
275    
276    2007-06-18 16:12  Douglas Bates <bates@stat.wisc.edu>
277    
278            * [r4472] src/Syms.h, src/init.c: Added Matrix_lengthSym
279            * [r4473] src/dgCMatrix.c: Modified dgCMatrix_colSums for sparseVector
280              result
281    
282    2007-06-16  Martin Maechler  <maechler@stat.math.ethz.ch>
283    
284            * R/kronecker.R: fix typo (could lead to inf.recursion)
285            * test/simple.R: testing that
286    
287            * R/sparseMatrix.R (prSpMatrix): change to be used as print()
288            method as well (which can have arguments, show() can't).
289    
290    2007-06-16 15:52  Douglas Bates <bates@stat.wisc.edu>
291    
292            * [r4466] R/dgCMatrix.R, src/dgCMatrix.c, src/dgCMatrix.h, src/init.c:
293              added dgCMatrix_colSums for [col,row][Sums,Means]
294    
295    2007-06-15 23:15  Douglas Bates <bates@stat.wisc.edu>
296    
297            * [r4460] R/sparseMatrix.R, man/dgCMatrix-class.Rd, src/dgCMatrix.c,
298              src/dgCMatrix.h, src/init.c: added lm.fit.sparse (unexported),
299              coercion of "factor" to "dgCMatrix" and dgCMatrix_cholsol
300            * [r4461] R/AllClass.R, man/sparseMatrix-class.Rd: draft "indicators"
301              class
302            * [r4463] R/sparseMatrix.R, man/dgCMatrix-class.Rd,
303              man/sparseMatrix-class.Rd: Don't need an "indicators" class - use the
304              row names to store the levels - duh!  Added an example.
305    
306    2007-06-14  Martin Maechler  <maechler@stat.math.ethz.ch>
307    
308            * src/Csparse.c (Csparse_validate): check for *repeated* entries
309            thanks to example from Christian Buchta; with a test here:
310            * tests/simple.R:
311    
312    2007-06-07  Martin Maechler  <maechler@stat.math.ethz.ch>
313    
314            * R/Auxiliaries.R (callGeneric): another fix, needed for some cases
315            of colSums(*, sparseResult = TRUE)
316    
317    2007-06-06  Martin Maechler  <maechler@stat.math.ethz.ch>
318    
319            * R/lsparseMatrix.R, R/ldenseMatrix.R (all, any): change default to
320            'na.rm = FALSE' as "everywhere" else in R.
321    
322    2007-06-05 Douglas Bates <bates@stat.wisc.edu>
323    
324            * [r4421] src/CSparse_install.sh: Modify for new organization of
325              CSparse package
326            * [r4425] src/UFsparse_download.sh: Update to version 3.0.0 of
327              SuiteSparse
328            * [r4426] src/Makefile: add ./UFconfig to the include path for
329              compilation
330            * [r4427] src/cs.[ch]: update to CSparse version 2.2.0
331            * [r4428] inst/doc/UFsparse/* src/{AMD,CHOLMOD,COLAMD}/*
332              src/UFconfig/UFconfig.h: Update to version 3.0.0 of SuiteSparse
333    
334    2007-06-05  Martin Maechler  <maechler@stat.math.ethz.ch>
335    
336            * R/Auxiliaries.R (emptyColnames): + argument msg.if.not.empty, used in
337            * R/sparseMatrix.R (prSpMatrix): now gives a message about
338            suppressed column names.
339    
340    2007-06-04 17:13  Douglas Bates <bates@stat.wisc.edu>
341    
342            * [r4418] src/Csparse.c, src/HBMM.c, src/Mutils.c, src/Mutils.h,
343              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dgCMatrix.c,
344              src/dgeMatrix.c, src/dpoMatrix.c, src/dpoMatrix.h, src/dppMatrix.c,
345              src/dppMatrix.h, src/dsCMatrix.c, src/dspMatrix.c, src/dspMatrix.h,
346              src/dsyMatrix.c, src/dsyMatrix.h, src/dtpMatrix.c, src/dtrMatrix.c:
347              Remove warnings after change to const char* CHAR
348    
349    2007-06-04 17:11  Douglas Bates <bates@stat.wisc.edu>
350    
351            * [r4417] inst/include/Matrix_stubs.c, inst/include/cholmod.h: Corrected
352              type of M_cholmod_ssmult
353    
354    2007-06-03 14:42  Douglas Bates <bates@stat.wisc.edu>
355    
356            * [r4412] inst/include/Matrix_stubs.c, inst/include/cholmod.h,
357              src/init.c: Yet another cholmod export - cholmod_ssmult
358    
359    2007-05-23  Martin Maechler  <maechler@stat.math.ethz.ch>
360    
361            * NAMESPACE: exported drop0(), since
362            * man/drop0.Rd: I have seen several cases, I really wanted to use
363            it, so our users may want too.
364    
365    2007-05-22  Martin Maechler  <maechler@stat.math.ethz.ch>
366    
367            * man/colSums.Rd: separately document colSums() etc, since these
368            have the extra argument 'sparseResult'.
369    
370    2007-05-21  Martin Maechler  <maechler@stat.math.ethz.ch>
371    
372            * R/sparseMatrix.R (spMatrix): utility (T)sparse Matrix constructor;
373            * man/spMatrix.Rd: docu., including examples
374    
375            * R/Auxiliaries.R (sp.colMeans): etc, using a patched callGeneric(),
376            in order to make colMeans() etc fast *and* correct.
377            * R/sparseVector.R (replSPvec): "[<-" functionality for
378            sparseVectors; tested in
379            * tests/simple.R:
380    
381    2007-05-19  Martin Maechler  <maechler@stat.math.ethz.ch>
382    
383            * R/sparseMatrix.R (print.sparseSummary): and summary() method for
384            (very) sparse Matrices; output similar to Matlab's print().
385    
386    2007-05-17  Douglas Bates  <bates@stat.wisc.edu>
387    
388            * src/HBMM.c (Matrix_writeMatrixMarket): Write 1-based, not
389            0-based, indices (Jose Quesada <quesada@gmail.com>).
390    
391    2007-05-16  Douglas Bates  <bates@stat.wisc.edu>
392    
393            * R/CHMfactor.R: Added solve methods for a CHMfactor object.
394    
395    2007-05-16  Martin Maechler  <maechler@stat.math.ethz.ch>
396    
397            * R/Auxiliaries.R (sparsapply): new utility, much faster than
398            tapply1() for large sparse matrices.
399    
400    2007-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
401    
402            * R/Matrix.R (dim<-): reshape now via sparseVector.
403    
404            * R/sparseVector.R: methods and function for
405            * R/AllClass.R: new "sparseVector" class and daughters.
406            * NAMESPACE: export new classes
407    
408    2007-05-14  Martin Maechler  <maechler@stat.math.ethz.ch>
409    
410            * DESCRIPTION (Version): 0.99875-1
411            * src/Makefile.win: also remove Lapack code from here (cf. 04-25).
412    
413    2007-05-11  Martin Maechler  <maechler@stat.math.ethz.ch>
414    
415            * R/Tsparse.R ([, Tsparse): fix last case: *duplicated*, symmetric
416            indexing
417            * tests/indexing.R: test set for that.
418    
419    2007-05-08  Martin Maechler  <maechler@stat.math.ethz.ch>
420    
421            * R/Tsparse.R (replTmat): fix the case of *duplicated* index
422            entries.
423            * tests/indexing.R(out): add regression test for it
424    
425    2007-04-30  Martin Maechler  <maechler@stat.math.ethz.ch>
426    
427            * R/(l(dense|sparse))?Matrix.R (!): use 'x', not 'e1' as argument
428            name for "!" method definitions.
429    
430    2007-04-26  Martin Maechler  <maechler@stat.math.ethz.ch>
431    
432            * R/Tsparse.R (intI): new utility, used for "[" :
433                    Cleanup up there, and fixes for duplicated indices - more TODO!
434    
435            * tests/indexing.R(out): more tests
436    
437  2007-04-25  Douglas Bates  <bates@stat.wisc.edu>  2007-04-25  Douglas Bates  <bates@stat.wisc.edu>
438    
439          * 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 442 
442          * src/init.c,inst/include/{Matrix_stubs.c,cholmod.h}:export          * src/init.c,inst/include/{Matrix_stubs.c,cholmod.h}:export
443          cholmod_factorize_p (used in lme4 for GLMMs and NLMMs).          cholmod_factorize_p (used in lme4 for GLMMs and NLMMs).
444    
445    2007-04-21  Martin Maechler  <maechler@stat.math.ethz.ch>
446    
447            * R/Matrix.R (image): method for all Matrices, not just sparse ones.
448    
449    2007-04-17  Martin Maechler  <maechler@stat.math.ethz.ch>
450    
451            * R/Auxiliaries.R (tapply1): unname(.) -> colSums() etc don't end
452            up with extraneous names '0'...'<n-1>'
453    
454  2007-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>  2007-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
455    
456          * R/dgTMatrix.R (mat2dgT): care about NAs          * R/dgTMatrix.R (mat2dgT): care about NAs

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