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revision 1852, Mon May 21 16:42:35 2007 UTC revision 2157, Tue Mar 25 15:00:01 2008 UTC
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1    2008-03-25  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * DESCRIPTION (Version,Date): 0.999375-8
4    
5            * R/diagMatrix.R (Ops): fix newly introduce bug in <.di> o <numeric>
6    
7            * inst/test-tools.R (isValid): new utility, used much in
8            * tests/simple.R:
9    
10            * man/BunchKaufman-methods.Rd: added too
11    
12    2008-03-24  Martin Maechler  <maechler@stat.math.ethz.ch>
13    
14            * R/dsyMatrix.R: add BunchKaufman() methods.
15            * R/dspMatrix.R:
16    
17            * src/init.c: add dsyMatrix_trf
18    
19    2008-03-23  Douglas Bates <bates@stat.wisc.edu>
20    
21            * DESCRIPTION (Version): release 0.999375-7
22            * src/CHMfactor.c (CHMfactor_update): fix
23    
24    2008-03-22  Martin Maechler  <maechler@stat.math.ethz.ch>
25    
26            * src/dsCMatrix.c (dsCMatrix_LDL_D): cleanup, also using
27            internal_chm_factor().
28    
29            * R/AllGeneric.R: do *not* define a "chol" generic
30                    (but rather use the implicit one *without* making pivot
31                    part of the signature)
32            * R/*.R: drop the 'pivot' from chol's signature and make
33                    'pivot=FALSE' a default argument of method definitions.
34    
35            * .Rbuildignore: add 'wrld_1deg': I.e. do not put it into released
36            version of Matrix
37    
38    2008-03-18  Martin Maechler  <maechler@stat.math.ethz.ch>
39    
40            * R/Tsparse.R (.T.2.n): drop 0's before coercion to "nMatrix"
41    
42            * R/sparseMatrix.R (is.na): new simple method
43            * R/denseMatrix.R (is.na): ditto.
44    
45            * R/diagMatrix.R (.symDiagonal): newly exported utility.
46    
47            * R/diagMatrix.R (Ops): <diag> * <numeric> should not become dgeMatrix!
48    
49            * src/UFsparse_download.sh: -->
50            * src/CHOLMOD/: update to CHOLMOD version 1.6 (Nov.2007)
51    
52    2008-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
53    
54            * src/dsCMatrix.c (dsCMatrix_LDL_D): even faster utility with same
55            functionality; barely tested in
56            * tests/factorizing.R
57    
58            * src/Csparse.c (diag_tC): new functionality to enable faster
59            determinant(<dsCMatrix>, .) in
60            * R/dsCMatrix.R
61    
62    2008-03-17 18:53  Douglas Bates <bates@stat.wisc.edu>
63    
64            * R/CHMfactor.R, inst/include/Matrix.h, inst/include/Matrix_stubs.c,
65              src/CHMfactor.c, src/CHMfactor.h,
66              man/CHMfactor-class.Rd, src/init.c, tests/factorizing.R:
67              Log-determinant of the parent matrix from a CHMfactor object as
68              chm_factor_ldetL2; documentation and support
69    
70    2008-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
71    
72            * R/dsCMatrix.R: enable determinant(<dsCMatrix>, .) via chol(.)
73    
74    2008-03-14  Martin Maechler  <maechler@stat.math.ethz.ch>
75    
76            * R/dsCMatrix.R: setAs(., "dsCMatrix") but with a deprecation
77            warning.
78    
79    2008-03-13  Martin Maechler  <maechler@stat.math.ethz.ch>
80    
81            * DESCRIPTION (Version, Date): bug-fix release 0.999375-6
82    
83            * R/diagMatrix.R (diag2tT.u): utility to be smarter in
84              <diagonal> o <sparse_triangular>
85              setAs(., "nMatrix") added.
86    
87            * R/diagMatrix.R (Diagonal): Diagonal(4, x=3) now works too
88    
89            * R/Auxiliaries.R (.diagU2N): more careful coercion in 2 steps
90                    new argument 'checkDense = FALSE'.
91    
92    
93    2008-03-07  Martin Maechler  <maechler@stat.math.ethz.ch>
94    
95            * src/dgeMatrix.c (dgeMatrix_exp): fix the octave-origin bug in the
96            back-permutation of the matrix exponential.
97    
98            * tests/matr-exp.R: test the fix (for an example where expm() was wrong).
99    
100            * DESCRIPTION (Date,Version): ready to release 0.999375-5
101    
102            * tests/simple.R: testing diagN2U
103    
104    2008-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
105    
106            * R/Auxiliaries.R (diagN2U): interface to
107    
108            * src/Csparse.c (Csparse_diagN2U): .Call()able SEXP version of chm_diagN2U()
109    
110            * tests/matprod.R: test for triangularity preserving <dtC> %*% <dtC>
111    
112    2008-03-05  Martin Maechler  <maechler@stat.math.ethz.ch>
113    
114            * src/chm_common.c (chm_diagN2U): new utility.
115    
116            * src/Csparse.c (Csparse_Csparse_crossprod, Csparse_Csparse_prod):
117            make use of chm_diagN2U() and hence now preserve triangularity and
118            unit-triangularity.
119    
120            * DESCRIPTION (LicenseDetails): new; such that 'License:' becomes "canonical"
121    
122    2008-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
123    
124            * R/diagMatrix.R (subDiag): fix when x[..] became a vector
125    
126            * src/Tsparse.c (Tsparse_diagU2N): new utility, necessary for e.g.
127            * src/Csparse.c (Csparse_crossprod): use [CT]sparse_diagU2N() !!
128    
129            * R/Auxiliaries.R (.diagU2N): make use of new Tsparse_diagU2N
130    
131            * R/Ops.R ("-" (<sparseMatrix>)): use diagU2N()
132    
133            * src/chm_common.c (AS_CHM_FINISH): add note about problem
134            for triangular (diag = "U").
135    
136    2008-02-21  Martin Maechler  <maechler@stat.math.ethz.ch>
137    
138            * R/Auxiliaries.R (as_Csparse2): drop this, replacing by
139            * R/bind.R:  .Call(dense_to_Csparse, *)
140    
141    2008-02-20  Martin Maechler  <maechler@stat.math.ethz.ch>
142    
143            * R/Matrix.R (Matrix): no longer use coercions to specific classes
144                    (since we are discouraging them in user code).
145    
146            * tests/*.R: also replaces coercions to specific classes by
147            coercions to super classes.
148    
149            * R/denseMatrix.R (.dense2C): simplified by using forceSymmetric()
150    
151    
152    2008-02-19  Martin Maechler  <maechler@stat.math.ethz.ch>
153    
154            * man/CAex.Rd: example: coerce to symmetric*, not dsC*
155    
156            * src/dense.c (dense_band): generalized from ddense_band
157    
158            * R/ddenseMatrix.R (.trilDense,.triuDense, .bandDense):
159              now for "denseMatrix" (instead of just "ddense*"); much
160              simplified setMethod()s for these.
161    
162            * src/dense.c (dense_to_symmetric): generalized from ddense_*
163    
164    2008-02-18  Martin Maechler  <maechler@stat.math.ethz.ch>
165    
166            * R/AllGeneric.R: forceSymmetric() generic: fast no-checking
167            version of as(*, "symmetricMatric").
168    
169            * src/dense.c (ddense_to_symmetric): add 'symm_test' argument, and
170            * R/symmetricMatrix.R: set it TRUE in coercion to "symmetricMatrix"
171    
172    2008-02-16  Martin Maechler  <maechler@stat.math.ethz.ch>
173    
174            * R/Matrix.R (subset.ij): utility, as first step to faster
175               M [ <ij-matrix> ] indexing.
176    
177            * R/Matrix.R (.M.sub.i.logical): M[ <logical> ] : try better.
178    
179            * src/dense.c (ddense_symmpart, ddense_skewpart): new functions
180            for more efficient symmpart() and skewpart() methods.
181    
182            * src/Mutils.c (equal_string_vectors): utility
183    
184            * src/dense.c (ddense_to_symmetric): new function used in
185    
186            * R/symmetricMatrix.R: setAs(., "symmetricMatrix")
187    
188            * R/sparseMatrix.R, et_al (isSymmetric): add '...' to formals, in
189            order to match the generic (and evade .local(..)).
190    
191            * R/dsCMatrix.R: dgC -> dsC: use C code!
192    
193            * NAMESPACE, R/AllGeneric.R (symmpart, skewpart): new functions
194            as per TODO
195    
196            * R/Auxiliaries.R (setZero, all0Matrix): new utilities
197    
198            * R/symmetricMatrix.R: obvious symmpart(), skewpart() methods
199    
200    
201    2008-02-15  Martin Maechler  <maechler@stat.math.ethz.ch>
202    
203            * R/Ops.R (.Arith.Csparse): use diagU2N when needed in triangular
204    
205            * R/Auxiliaries.R (non0.i): take out of non0ind
206    
207            * R/ddenseMatrix.R (.trilDense, .triuDense, .bandDense):
208            make tril(), triu(), band() work for "matrix" and all "dense*"
209    
210            * R/triangularMatrix.R (.tri[lu].tr): need .diagU2N(*)
211            * tests/simple.R: test the fix above
212    
213            * R/sparseMatrix.R ([): simplification: no coerce to <general>
214                    before we use as(., <Tsparse>)[...] anyway
215    
216            * R/Rsparse.R (.viaC.to.R): mostly instead of .viaC.to.dgR()
217    
218            * R/triangularMatrix.R (isTriangular): methods for all subclasses
219            instead of "triangularMatrix" -- just to disambiguate
220    
221    2008-02-14  Martin Maechler  <maechler@stat.math.ethz.ch>
222    
223            * tests/Class+Meth.R (dotestMat): add m[FALSE, FALSE] { <-> TODO}
224            * tests/indexing.R: example that fails above
225    
226    2008-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
227    
228            * R/Matrix.R (.M.sub.i.2col): fix for logical matrix indexing
229            * R/Tsparse.R (.TM.sub.i.2col, .TM.repl.i.2col): ditto;
230                    now, M[lower.tri(M)] and  M[lower.tri(M)] <- v  work better
231    
232            * src/Tsparse.c (Tsparse_to_tCsparse): new fast utility.
233            * src/Tsparse.h, init.c: ditto
234            * R/Auxiliaries.R (isTriT): new; faster than going via Csparse
235                 both isTriC() and isTriT() now return TRUE with "kind" or FALSE.
236            * R/sparseMatrix.R (isTriangular): hence simplified
237    
238    2008-01-24  Martin Maechler  <maechler@stat.math.ethz.ch>
239    
240            * R/Ops.R (.Arith.Csparse): new utility factored out of former
241              <dgC> o <dgC>, extended for triangular and also used in  <dtC> o <dtC>.
242    
243    2008-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
244    
245            * tests/factorizing.R (checkSchur): and more tests for checking Schur()
246    
247            * inst/test-tools.R (isOrthogonal): new function; also file restructured
248    
249    2008-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
250    
251            * R/ngTMatrix.R: allow as(<numeric matrix>, "ngTMatrix") and hence
252            coercion to "nMatrix" and "pMatrix"
253    
254            * R/AllClass.R: "Schur" class;  "number" class union
255            * man/number-class.Rd:
256            * man/Schur-class.Rd:
257    
258            * R/eigen.R (.dgeSchur): utility, and return "Schur" class
259            (.simpleSchur): Schur() method for diagonal matrices
260            (.triSchur):    Schur() method for triangular matrices
261            (Schur.sym):    Schur() for symmetric matrices {building on eigen()}.
262    
263    
264    2008-01-21  Martin Maechler  <maechler@stat.math.ethz.ch>
265    
266            * src/dgCMatrix.c (dgCMatrix_QR): set @Dim slot (as per doc)
267    
268    2008-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
269    
270            * R/CHMfactor.R (solve): method for b="numeric", but also b="ANY"
271                    in order to ensure 'system = *' is not lost;
272                    formals()$system instead of cut&paste.
273            * tests/factorizing.R: test solve(<CHM..>, <numeric>)
274    
275    2008-01-11  Martin Maechler  <maechler@stat.math.ethz.ch>
276    
277            * DESCRIPTION (Date): make ready for release --> 0.999375-4
278    
279            * R/dgeMatrix.R: fix rcond() method for "dgeMatrix".
280    
281    2007-12-08  Martin Maechler  <maechler@stat.math.ethz.ch>
282    
283            * R/pMatrix.R: as(*, "matrix") now returns 0/1 *integer* matrix,
284                    and hence does as.vector(.).
285            * man/pMatrix-class.Rd: docs
286            * R/sparseMatrix.R: fix for printing "integer sparse"
287    
288            * tests/Class+Meth.R (tstMatrixClass): test M[FALSE], M[2] etc
289    
290            * R/Matrix.R and others: use "exact" function argument list for
291                    both "["   : (x, i,j, ..., drop)
292                    and  "[<-" : (x, i,j, ..., value)
293    
294            * R/denseMatrix.R: M[i] and M[i] <- v  (i vector) now work
295            * R/Tsparse.R (replTmat):    ditto
296            * R/diagMatrix.R (replDiag): ditto
297            * R/Csparse.R (replCmat):    ditto {was it worth the pain?}
298            * tests/indexing.R: testing the above
299    
300    2007-12-07  Martin Maechler  <maechler@stat.math.ethz.ch>
301    
302            * R/sparseMatrix.R (cov2cor): method for sparse matrices
303    
304            * R/diagMatrix.R ([<-): fix   D[ cbind(i,j) ] <- v
305    
306            * R/bind2.R: fix for Rsparse* and rbind2(dense,dense)
307    
308            * tests/Class+Meth.R: test cbind2, rbind2  and  diag<-
309    
310    2007-12-06  Martin Maechler  <maechler@stat.math.ethz.ch>
311    
312            * R/Matrix.R: "generic" cov2cor() method
313    
314            * R/nearPD.R: new 'only.values', 'keepDiag' arguments;
315                    speed up Q %*% D %*% t(Q)
316            * tests/dpoMatrix.R: test nearPD()
317    
318    2007-12-05  Doug Bates and Martin Maechler
319    
320            * R/sparseMatrix.R: xtabs(*, sparse=.) function; an extention of
321            stats::xtabs() allowing to create sparse matrices.
322    
323    2007-10-08  Martin Maechler  <maechler@stat.math.ethz.ch>
324    
325            * DESCRIPTION (Version): *-4 (released *-3 two days ago)
326    
327    2007-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
328    
329            * R/pMatrix.R: solve(<Matrix>, <pMatrix>)
330    
331    2007-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
332    
333            * R/LU.R: solve() method for "denseLU"
334    
335    2007-10-01  Martin Maechler  <maechler@stat.math.ethz.ch>
336    
337            * DESCRIPTION (Version): 0.999375-3 preparing for release
338    
339            * R/AllGeneric.R: simplify  if(.) .. else .. for R <= 2.5.1
340    
341            * R/Matrix.R (Matrix): .Internal(matrix(..)) different for R >= 2.7.0
342    
343    2007-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
344    
345            * R/pMatrix.R (.m.mult.pMat): fix <matrix> %*% <pMatrix>,
346              thanks to Kasper Kristensen.
347            * tests/matprod.R: regression test for that.
348    
349    2007-09-23 17:32  Douglas Bates <bates@stat.wisc.edu>
350    
351            * [r4778] R/AllGeneric.R: Check R version before defining generics for
352              primitives
353    
354    2007-09-13  Martin Maechler  <maechler@stat.math.ethz.ch>
355    
356            * R/denseMatrix.R (rcond): method
357            * R/sparseQR.R (rcond): method, use x or t(x)
358    
359    2007-09-12  Martin Maechler  <maechler@stat.math.ethz.ch>
360    
361            * R/dgeMatrix.R (rcond): method: work via qr.R() for non-square
362            matrices.
363            * R/sparseMatrix.R: Ditto for all other rcond() method definitions.
364    
365            * man/rcond.Rd: mention the more general definition, and add
366            example for non-square matrices.
367    
368            * man/chol.Rd: new file, for the S4 chol() generic and all methods.
369    
370    2007-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
371    
372            * R/sparseQR.R: add qr.R() method [to be used for rcond()]
373    
374    2007-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
375    
376            * R/Matrix.R ([<-): add (Matrix,missing,ANY,Matrix) etc
377            * tests/indexing.R: add new regression for the above cases.
378    
379    2007-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
380    
381            * src/Mutils.h (__sun): clause for alloca.h on Solaris
382    
383    2007-08-16  Martin Maechler  <maechler@stat.math.ethz.ch>
384    
385            * DESCRIPTION (Date, Version): 0.999375-2
386    
387    2007-08-15  Martin Maechler  <maechler@stat.math.ethz.ch>
388    
389            * R/HBMM.R (readMM): make work for pattern matrices as well
390    
391    2007-08-14 13:07  Douglas Bates <bates@stat.wisc.edu>
392    
393            * [r4730] src/Mutils.h: declare alloca
394            * [r4734] NAMESPACE, R/AllGeneric.R, R/Csparse.R, R/HBMM.R, R/Tsparse.R,
395              R/dgCMatrix.R, R/dgTMatrix.R, R/dsCMatrix.R, R/dsTMatrix.R,
396              man/externalFormats.Rd, src/Csparse.c, src/Csparse.h, src/DEPS.mkf,
397              src/HBMM.c, src/HBMM.h, src/Mutils.h, src/SOURCES_C.mkf, src/init.c,
398              src/mmio.c, src/mmio.h: Remove deprecated function writeHB and its
399              methods; switch writeMM to use CHOLMOD code; repair readMM
400    
401    2007-08-14  Martin Maechler  <maechler@stat.math.ethz.ch>
402    
403            * R/nearPD.R, man/nearPD.Rd (nearPD): new function built on Jens
404            Oehlschlaegel's ... result type still to be discussed!
405    
406    2007-08-10  Martin Maechler  <maechler@stat.math.ethz.ch>
407    
408            * man/image-methods.Rd: new, combining all image() methods
409    
410    2007-08-09  Martin Maechler  <maechler@stat.math.ethz.ch>
411    
412            * R/dgCMatrix.R: define qr() and lu() methods for "sparseMatrix"
413            to work via dgC...
414    
415            * R/Matrix.R (Matrix): special treatment for "table" (S3)
416    
417    2007-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
418    
419            * R/dgTMatrix.R (image): change defaults to
420                    aspect = "iso", colorkey = FALSE
421    
422    2007-08-06  Martin Maechler  <maechler@stat.math.ethz.ch>
423    
424            * src/dsyMatrix.c (dsyMatrix_matrix_mm): 'b' might be matrix;
425            must copy its *expanded* x slot before LAPACK call.
426    
427            * tests/matprod.R: test the last days' changes.
428    
429    2007-08-06 16:43  Douglas Bates <bates@stat.wisc.edu>
430    
431            * [r4712] inst/include/Matrix_stubs.c: Change R_cholmod_printf in stubs
432              as well as in sources
433            * [r4713] src/dsyMatrix.c: Duplicate the contents of the RHS before
434              Lapack call
435    
436    2007-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
437    
438            * R/Matrix.R (%*%, crossprod, tcrossprod): add method for
439                    ("Matrix", "matrix") which is needed in some cases.
440            Ditto for solve().
441    
442            * R/colSums.R (.as.dge.Fun): need ddenseMatrix methods to avoid
443            infinite recursion in dispatch for some cases.
444    
445    2007-08-02 08:48  Martin Maechler <maechler@stat.math.ethz.ch>
446    
447            * [r4693] src/chm_common.c: R_cholmod_printf() instead of Rprintf() just
448              so pointers match
449    
450    2007-08-02  Martin Maechler  <maechler@stat.math.ethz.ch>
451    
452            * DESCRIPTION (Date): set ready for release -- 0.999375-1
453    
454    2007-08-01 15:44  Douglas Bates <bates@stat.wisc.edu>
455    
456            * [r4686] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
457              src/chm_common.c, src/chm_common.h: Change API for
458              numeric_as_chm_dense and N_AS_CHM_DN
459    
460    2007-08-01  Martin Maechler  <maechler@stat.math.ethz.ch>
461    
462            * src/dtrMatrix.c (dtrMatrix_matrix_mm): fix dimensionality check (!)
463            * tests/matprod.R: regr.test for it
464    
465    2007-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
466    
467            * R/dMatrix.R: fix from Brian for   Math2(., digits = "missing")
468            * tests/group-methods.R: and regression-test it
469    
470    2007-07-19 19:45  Douglas Bates <bates@stat.wisc.edu>
471    
472            * [r4642] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
473              inst/include/cholmod.h, src/chm_common.c, src/init.c: Export
474              triplet_to_sparse, documentation, use typedefs
475    
476    2007-07-18  Martin Maechler  <maechler@stat.math.ethz.ch>
477    
478            * man/dpoMatrix-class.Rd: added 'corMatrix' example
479    
480            * src/dsyMatrix.[ch] (dsyMatrix_as_matrix): new 'keep_dimnames' arg
481            * src/dtrMatrix.[ch] (dtrMatrix_as_matrix): ditto
482            * src/init.c, R/dsyMatrix.R, R/dtrMatrix.R, R/lgTMatrix.R: ditto
483    
484            * R/lsparseMatrix.R: bug fix in "all" method
485            * R/Ops.R (.do.Logic.lsparse): "|" bug in borderline case
486    
487            * R/dsyMatrix.R (coerce->dsTMatrix): (i,j) slots should *not* have names
488            * R/ngTMatrix.R (coerce->ngTMatrix): ditto;
489                    + matrix |-> nMatrix coercion
490            * R/pMatrix.R: + setAs()  to dMatrix and from nMatrix
491            * man/pMatrix-class.Rd: ditto
492    
493            * R/Matrix.R (Summary): method for non-dMatrix
494    
495            * tests/Class+Meth.R (extraValid): new check about "dirty" slots
496            * tests/Class+Meth.R (tstMatrixClass): test norm(.);
497                    test all Summary methods.
498    
499    2007-07-16  Martin Maechler  <maechler@stat.math.ethz.ch>
500    
501            * R/dgeMatrix.R (norm, rcond): methods for 'matrix'
502    
503    2007-07-14  Martin Maechler  <maechler@stat.math.ethz.ch>
504    
505            * R/sparseMatrix.R (norm): simple methods for sparseMatrix
506    
507            * R/pMatrix.R (t?crossprod): methods for pMatrix
508    
509    2007-07-10  Douglas Bates  <bates@stat.wisc.edu>
510    
511            * src/dgeMatrix.c (dgeMatrix_colsums): Get the logic straight.
512    
513    2007-07-09 20:45  Douglas Bates <bates@stat.wisc.edu>
514    
515            * [r4579] src/dgeMatrix.c: Untangle horrible code in dgeMatrix_colsums
516              trying to fix a subtle bug - which has been somewhere else.
517    
518    2007-07-09 19:43  Martin Maechler <maechler@stat.math.ethz.ch>
519    
520            * [r4578] src/dgeMatrix.c: "cleaned" dgeMatrix_colsums() - but did not
521              solve the bug
522    
523    2007-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
524    
525            * src/dgCMatrix.c (compressed_to_TMatrix):
526    
527    2007-07-07  Martin Maechler  <maechler@stat.math.ethz.ch>
528    
529            * src/Csparse.c (Rsparse_validate): new, to have some validity
530            checking for RsparseMatrix
531            * src/dgCMatrix.c (xRMatrix_validate): ditto
532            * src/dtCMatrix.c (tRMatrix_validate): ditto
533    
534    2007-07-07  Douglas Bates <bates@stat.wisc.edu>
535    
536            * [r4567] R/AllClass.R: Slots already in RsparseMatrix were redefined in
537              lgRMatrix
538            * [r4568] DESCRIPTION: Prepare for bug-fix release
539            * [r4570] src/CHOLMOD/Check/cholmod_write.c: Include cholmod_matrixops.h
540              for declaration of cholmod_symmetry
541    
542    2007-07-06  Martin Maechler  <maechler@stat.math.ethz.ch>
543    
544            * DESCRIPTION (Version): 0.999375 merged into the trunk; ready for
545            release.
546    
547    2007-07-06 14:11  Douglas Bates <bates@stat.wisc.edu>
548    
549            * [r4559] src/iohb.c, src/iohb.h: Remove Harwell-Boeing input/output
550              functions - no longer used
551            * [r4560] src/HBMM.c, src/Mutils.c, src/dgTMatrix.c, src/dgeMatrix.c,
552              src/dspMatrix.c, src/dsyMatrix.c, src/dtCMatrix.c,
553              src/factorizations.c, src/sparseQR.c: Replace most calls to Calloc by
554              Alloca
555    
556    2007-07-06 13:14  Martin Maechler <maechler@stat.math.ethz.ch>
557    
558            * [r4558] inst/doc/Comparisons.Rnw, src/CHMfactor.c, src/Csparse.c,
559              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dense.c,
560              src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c, src/sparseQR.c,
561              src/t_gCMatrix_colSums.c: more R_CheckStack()s
562    
563    2007-07-05 18:12  Douglas Bates <bates@stat.wisc.edu>
564    
565            * [r4550] inst/include/Matrix.h: Add the macro N_AS_CHM_DN to "alloca"
566              the required amount of memory then call M_numeric_as_chm_dense.
567            * [r4556] src/Mutils.h, src/dgCMatrix.c: Define and use the Alloca macro
568              (like Calloc but calling alloca)
569    
570    2007-07-05  Martin Maechler  <maechler@stat.math.ethz.ch>
571    
572            * R/sparseMatrix.R (printSpMatrix): renamed from prSpMatrix()
573            and extended with more sophisticated 'col.names' option.
574            * NAMESPACE: export  printSparseMatrix()
575            * man/printSpMatrix.Rd: document, incl. examples
576    
577    2007-07-04 16:21  Douglas Bates <bates@stat.wisc.edu>
578    
579            * [r4543] src/cs_utils.c, src/cs_utils.h, src/dgCMatrix.c,
580              src/dtCMatrix.c, src/sparseQR.c: CSP typedef for *cs and macro
581              AS_CSP. API change - pass the empty structure to Matrix_as_cs.
582    
583    2007-07-04  Martin Maechler  <maechler@stat.math.ethz.ch>
584    
585            * DESCRIPTION (Version): 0.99875-4
586    
587            * tests/Class+Meth.R (tstMatrixClass): add dimnames, and hence test
588            some dimnames perservation.
589    
590            * R/dsTMatrix.R (t-method): keep dimnames
591            * R/dtTMatrix.R:  ditto
592    
593            * R/sparseMatrix.R (prSpMatrix): print colnames when non-trivial
594            and ncol(.) < 10
595    
596            * src/cs_utils.c: drop check_class() and use Matrix_check_class()
597            from Mutils.h
598    
599            * src/lgCMatrix.c ([ln]csc_to_matrix): no longer lose dimnames,
600            e.g. in as(<ngCMatrix>, "matrix")
601    
602    2007-07-01 13:27  Douglas Bates <bates@stat.wisc.edu>
603    
604            * [r4529] .: Create a branch for the API changes from the 0.99875
605              series to the 0.999375 series
606            * [r4530] DESCRIPTION, inst/include/Matrix.h,
607              inst/include/Matrix_stubs.c, src/CHMfactor.c, src/Csparse.c,
608              src/Mutils.h, src/Tsparse.c, src/chm_common.c, src/chm_common.h,
609              src/dense.c, src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c,
610              src/t_gCMatrix_colSums.c: API change - pass the empty structure to the
611              as_cholmod_x functions
612    
613    2007-06-30 09:05  Martin Maechler <maechler@stat.math.ethz.ch>
614    
615            * [r4527] trunk/Matrix/DESCRIPTION, trunk/Matrix/NAMESPACE,
616              trunk/Matrix/inst/doc/Comparisons.Rnw: add session- and hardware-info
617              to Comparisons
618    
619    >>>>>>> .merge-right.r4561
620    2007-06-29  Martin Maechler  <maechler@stat.math.ethz.ch>
621    
622            * DESCRIPTION (Version): 0.99875-3 ready to be released.
623    
624            * R/sparseMatrix.R (spMatrix): make spMatrix(3,4) working
625    
626            * R/AllGeneric.R: set "Math" (and "Math2") group generics in a way
627            that should also work in a future version of R.
628    
629    2007-06-21  Martin Maechler  <maechler@stat.math.ethz.ch>
630    
631            * NAMESPACE, R/AllClass.R: "xsparseVector" class union.
632    
633            * R/sparseVector.R: more *sparseVector coercions, notably for
634            non - double ones.
635    
636    2007-06-19  Martin Maechler  <maechler@stat.math.ethz.ch>
637    
638            * R/colSums.R: new file for all (col|row)(Sums|Means) methods,
639              notably the new ones building on the new .Call(.)s:
640    
641            * src/dgCMatrix.c (DEF_gCMatrix_COLSUMS): use to define
642            all 4 of [dlin]gCMatrix_colSums().
643    
644    2007-06-18 16:12  Douglas Bates <bates@stat.wisc.edu>
645    
646            * [r4472] src/Syms.h, src/init.c: Added Matrix_lengthSym
647            * [r4473] src/dgCMatrix.c: Modified dgCMatrix_colSums for sparseVector
648              result
649    
650    2007-06-16  Martin Maechler  <maechler@stat.math.ethz.ch>
651    
652            * R/kronecker.R: fix typo (could lead to inf.recursion)
653            * test/simple.R: testing that
654    
655            * R/sparseMatrix.R (prSpMatrix): change to be used as print()
656            method as well (which can have arguments, show() can't).
657    
658    2007-06-16 15:52  Douglas Bates <bates@stat.wisc.edu>
659    
660            * [r4466] R/dgCMatrix.R, src/dgCMatrix.c, src/dgCMatrix.h, src/init.c:
661              added dgCMatrix_colSums for [col,row][Sums,Means]
662    
663    2007-06-15 23:15  Douglas Bates <bates@stat.wisc.edu>
664    
665            * [r4460] R/sparseMatrix.R, man/dgCMatrix-class.Rd, src/dgCMatrix.c,
666              src/dgCMatrix.h, src/init.c: added lm.fit.sparse (unexported),
667              coercion of "factor" to "dgCMatrix" and dgCMatrix_cholsol
668            * [r4461] R/AllClass.R, man/sparseMatrix-class.Rd: draft "indicators"
669              class
670            * [r4463] R/sparseMatrix.R, man/dgCMatrix-class.Rd,
671              man/sparseMatrix-class.Rd: Don't need an "indicators" class - use the
672              row names to store the levels - duh!  Added an example.
673    
674    2007-06-14  Martin Maechler  <maechler@stat.math.ethz.ch>
675    
676            * src/Csparse.c (Csparse_validate): check for *repeated* entries
677            thanks to example from Christian Buchta; with a test here:
678            * tests/simple.R:
679    
680    2007-06-07  Martin Maechler  <maechler@stat.math.ethz.ch>
681    
682            * R/Auxiliaries.R (callGeneric): another fix, needed for some cases
683            of colSums(*, sparseResult = TRUE)
684    
685    2007-06-06  Martin Maechler  <maechler@stat.math.ethz.ch>
686    
687            * R/lsparseMatrix.R, R/ldenseMatrix.R (all, any): change default to
688            'na.rm = FALSE' as "everywhere" else in R.
689    
690    2007-06-05 Douglas Bates <bates@stat.wisc.edu>
691    
692            * [r4421] src/CSparse_install.sh: Modify for new organization of
693              CSparse package
694            * [r4425] src/UFsparse_download.sh: Update to version 3.0.0 of
695              SuiteSparse
696            * [r4426] src/Makefile: add ./UFconfig to the include path for
697              compilation
698            * [r4427] src/cs.[ch]: update to CSparse version 2.2.0
699            * [r4428] inst/doc/UFsparse/* src/{AMD,CHOLMOD,COLAMD}/*
700              src/UFconfig/UFconfig.h: Update to version 3.0.0 of SuiteSparse
701    
702    2007-06-05  Martin Maechler  <maechler@stat.math.ethz.ch>
703    
704            * R/Auxiliaries.R (emptyColnames): + argument msg.if.not.empty, used in
705            * R/sparseMatrix.R (prSpMatrix): now gives a message about
706            suppressed column names.
707    
708    2007-06-04 17:13  Douglas Bates <bates@stat.wisc.edu>
709    
710            * [r4418] src/Csparse.c, src/HBMM.c, src/Mutils.c, src/Mutils.h,
711              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dgCMatrix.c,
712              src/dgeMatrix.c, src/dpoMatrix.c, src/dpoMatrix.h, src/dppMatrix.c,
713              src/dppMatrix.h, src/dsCMatrix.c, src/dspMatrix.c, src/dspMatrix.h,
714              src/dsyMatrix.c, src/dsyMatrix.h, src/dtpMatrix.c, src/dtrMatrix.c:
715              Remove warnings after change to const char* CHAR
716    
717    2007-06-04 17:11  Douglas Bates <bates@stat.wisc.edu>
718    
719            * [r4417] inst/include/Matrix_stubs.c, inst/include/cholmod.h: Corrected
720              type of M_cholmod_ssmult
721    
722    2007-06-03 14:42  Douglas Bates <bates@stat.wisc.edu>
723    
724            * [r4412] inst/include/Matrix_stubs.c, inst/include/cholmod.h,
725              src/init.c: Yet another cholmod export - cholmod_ssmult
726    
727    2007-05-23  Martin Maechler  <maechler@stat.math.ethz.ch>
728    
729            * NAMESPACE: exported drop0(), since
730            * man/drop0.Rd: I have seen several cases, I really wanted to use
731            it, so our users may want too.
732    
733    2007-05-22  Martin Maechler  <maechler@stat.math.ethz.ch>
734    
735            * man/colSums.Rd: separately document colSums() etc, since these
736            have the extra argument 'sparseResult'.
737    
738  2007-05-21  Martin Maechler  <maechler@stat.math.ethz.ch>  2007-05-21  Martin Maechler  <maechler@stat.math.ethz.ch>
739    
740          * R/sparseMatrix.R (spMatrix): utility (T)sparse Matrix constructor;          * R/sparseMatrix.R (spMatrix): utility (T)sparse Matrix constructor;

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