SCM

SCM Repository

[matrix] Diff of /pkg/ChangeLog
ViewVC logotype

Diff of /pkg/ChangeLog

Parent Directory Parent Directory | Revision Log Revision Log | View Patch Patch

revision 1624, Wed Oct 11 15:00:11 2006 UTC revision 2161, Sat Mar 29 14:08:25 2008 UTC
# Line 1  Line 1 
1    2008-03-29  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * DESCRIPTION (Version): 0.999375-9 --- need to release
4            for R-devel (and R 2.7.0 alpha soon).
5    
6            * R/AllGeneric.R (rcond): check for base::rcond instead of R version
7    
8            * R/sparseMatrix.R (summary): count NAs
9    
10    2008-03-28  Martin Maechler  <maechler@stat.math.ethz.ch>
11    
12            * R/AllGeneric.R: rcond(., norm) instead of rcond(., type), in
13            order to become compatible to new R 2.7.0 base::rcond().
14    
15    2008-03-25  Martin Maechler  <maechler@stat.math.ethz.ch>
16    
17            * DESCRIPTION (Version,Date): 0.999375-8 --- released to CRAN
18    
19            * R/diagMatrix.R (Ops): fix newly introduce bug in <.di> o <numeric>
20    
21            * inst/test-tools.R (isValid): new utility, used much in
22            * tests/simple.R:
23    
24            * man/BunchKaufman-methods.Rd: added too
25    
26    2008-03-24  Martin Maechler  <maechler@stat.math.ethz.ch>
27    
28            * R/dsyMatrix.R: add BunchKaufman() methods.
29            * R/dspMatrix.R:
30    
31            * src/init.c: add dsyMatrix_trf
32    
33    2008-03-23  Douglas Bates <bates@stat.wisc.edu>
34    
35            * DESCRIPTION (Version): release 0.999375-7
36            * src/CHMfactor.c (CHMfactor_update): fix
37    
38    2008-03-22  Martin Maechler  <maechler@stat.math.ethz.ch>
39    
40            * src/dsCMatrix.c (dsCMatrix_LDL_D): cleanup, also using
41            internal_chm_factor().
42    
43            * R/AllGeneric.R: do *not* define a "chol" generic
44                    (but rather use the implicit one *without* making pivot
45                    part of the signature)
46            * R/*.R: drop the 'pivot' from chol's signature and make
47                    'pivot=FALSE' a default argument of method definitions.
48    
49            * .Rbuildignore: add 'wrld_1deg': I.e. do not put it into released
50            version of Matrix
51    
52    2008-03-18  Martin Maechler  <maechler@stat.math.ethz.ch>
53    
54            * R/Tsparse.R (.T.2.n): drop 0's before coercion to "nMatrix"
55    
56            * R/sparseMatrix.R (is.na): new simple method
57            * R/denseMatrix.R (is.na): ditto.
58    
59            * R/diagMatrix.R (.symDiagonal): newly exported utility.
60    
61            * R/diagMatrix.R (Ops): <diag> * <numeric> should not become dgeMatrix!
62    
63            * src/UFsparse_download.sh: -->
64            * src/CHOLMOD/: update to CHOLMOD version 1.6 (Nov.2007)
65    
66    2008-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
67    
68            * src/dsCMatrix.c (dsCMatrix_LDL_D): even faster utility with same
69            functionality; barely tested in
70            * tests/factorizing.R
71    
72            * src/Csparse.c (diag_tC): new functionality to enable faster
73            determinant(<dsCMatrix>, .) in
74            * R/dsCMatrix.R
75    
76    2008-03-17 18:53  Douglas Bates <bates@stat.wisc.edu>
77    
78            * R/CHMfactor.R, inst/include/Matrix.h, inst/include/Matrix_stubs.c,
79              src/CHMfactor.c, src/CHMfactor.h,
80              man/CHMfactor-class.Rd, src/init.c, tests/factorizing.R:
81              Log-determinant of the parent matrix from a CHMfactor object as
82              chm_factor_ldetL2; documentation and support
83    
84    2008-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
85    
86            * R/dsCMatrix.R: enable determinant(<dsCMatrix>, .) via chol(.)
87    
88    2008-03-14  Martin Maechler  <maechler@stat.math.ethz.ch>
89    
90            * R/dsCMatrix.R: setAs(., "dsCMatrix") but with a deprecation
91            warning.
92    
93    2008-03-13  Martin Maechler  <maechler@stat.math.ethz.ch>
94    
95            * DESCRIPTION (Version, Date): bug-fix release 0.999375-6
96    
97            * R/diagMatrix.R (diag2tT.u): utility to be smarter in
98              <diagonal> o <sparse_triangular>
99              setAs(., "nMatrix") added.
100    
101            * R/diagMatrix.R (Diagonal): Diagonal(4, x=3) now works too
102    
103            * R/Auxiliaries.R (.diagU2N): more careful coercion in 2 steps
104                    new argument 'checkDense = FALSE'.
105    
106    
107    2008-03-07  Martin Maechler  <maechler@stat.math.ethz.ch>
108    
109            * src/dgeMatrix.c (dgeMatrix_exp): fix the octave-origin bug in the
110            back-permutation of the matrix exponential.
111    
112            * tests/matr-exp.R: test the fix (for an example where expm() was wrong).
113    
114            * DESCRIPTION (Date,Version): ready to release 0.999375-5
115    
116            * tests/simple.R: testing diagN2U
117    
118    2008-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
119    
120            * R/Auxiliaries.R (diagN2U): interface to
121    
122            * src/Csparse.c (Csparse_diagN2U): .Call()able SEXP version of chm_diagN2U()
123    
124            * tests/matprod.R: test for triangularity preserving <dtC> %*% <dtC>
125    
126    2008-03-05  Martin Maechler  <maechler@stat.math.ethz.ch>
127    
128            * src/chm_common.c (chm_diagN2U): new utility.
129    
130            * src/Csparse.c (Csparse_Csparse_crossprod, Csparse_Csparse_prod):
131            make use of chm_diagN2U() and hence now preserve triangularity and
132            unit-triangularity.
133    
134            * DESCRIPTION (LicenseDetails): new; such that 'License:' becomes "canonical"
135    
136    2008-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
137    
138            * R/diagMatrix.R (subDiag): fix when x[..] became a vector
139    
140            * src/Tsparse.c (Tsparse_diagU2N): new utility, necessary for e.g.
141            * src/Csparse.c (Csparse_crossprod): use [CT]sparse_diagU2N() !!
142    
143            * R/Auxiliaries.R (.diagU2N): make use of new Tsparse_diagU2N
144    
145            * R/Ops.R ("-" (<sparseMatrix>)): use diagU2N()
146    
147            * src/chm_common.c (AS_CHM_FINISH): add note about problem
148            for triangular (diag = "U").
149    
150    2008-02-21  Martin Maechler  <maechler@stat.math.ethz.ch>
151    
152            * R/Auxiliaries.R (as_Csparse2): drop this, replacing by
153            * R/bind.R:  .Call(dense_to_Csparse, *)
154    
155    2008-02-20  Martin Maechler  <maechler@stat.math.ethz.ch>
156    
157            * R/Matrix.R (Matrix): no longer use coercions to specific classes
158                    (since we are discouraging them in user code).
159    
160            * tests/*.R: also replaces coercions to specific classes by
161            coercions to super classes.
162    
163            * R/denseMatrix.R (.dense2C): simplified by using forceSymmetric()
164    
165    
166    2008-02-19  Martin Maechler  <maechler@stat.math.ethz.ch>
167    
168            * man/CAex.Rd: example: coerce to symmetric*, not dsC*
169    
170            * src/dense.c (dense_band): generalized from ddense_band
171    
172            * R/ddenseMatrix.R (.trilDense,.triuDense, .bandDense):
173              now for "denseMatrix" (instead of just "ddense*"); much
174              simplified setMethod()s for these.
175    
176            * src/dense.c (dense_to_symmetric): generalized from ddense_*
177    
178    2008-02-18  Martin Maechler  <maechler@stat.math.ethz.ch>
179    
180            * R/AllGeneric.R: forceSymmetric() generic: fast no-checking
181            version of as(*, "symmetricMatric").
182    
183            * src/dense.c (ddense_to_symmetric): add 'symm_test' argument, and
184            * R/symmetricMatrix.R: set it TRUE in coercion to "symmetricMatrix"
185    
186    2008-02-16  Martin Maechler  <maechler@stat.math.ethz.ch>
187    
188            * R/Matrix.R (subset.ij): utility, as first step to faster
189               M [ <ij-matrix> ] indexing.
190    
191            * R/Matrix.R (.M.sub.i.logical): M[ <logical> ] : try better.
192    
193            * src/dense.c (ddense_symmpart, ddense_skewpart): new functions
194            for more efficient symmpart() and skewpart() methods.
195    
196            * src/Mutils.c (equal_string_vectors): utility
197    
198            * src/dense.c (ddense_to_symmetric): new function used in
199    
200            * R/symmetricMatrix.R: setAs(., "symmetricMatrix")
201    
202            * R/sparseMatrix.R, et_al (isSymmetric): add '...' to formals, in
203            order to match the generic (and evade .local(..)).
204    
205            * R/dsCMatrix.R: dgC -> dsC: use C code!
206    
207            * NAMESPACE, R/AllGeneric.R (symmpart, skewpart): new functions
208            as per TODO
209    
210            * R/Auxiliaries.R (setZero, all0Matrix): new utilities
211    
212            * R/symmetricMatrix.R: obvious symmpart(), skewpart() methods
213    
214    
215    2008-02-15  Martin Maechler  <maechler@stat.math.ethz.ch>
216    
217            * R/Ops.R (.Arith.Csparse): use diagU2N when needed in triangular
218    
219            * R/Auxiliaries.R (non0.i): take out of non0ind
220    
221            * R/ddenseMatrix.R (.trilDense, .triuDense, .bandDense):
222            make tril(), triu(), band() work for "matrix" and all "dense*"
223    
224            * R/triangularMatrix.R (.tri[lu].tr): need .diagU2N(*)
225            * tests/simple.R: test the fix above
226    
227            * R/sparseMatrix.R ([): simplification: no coerce to <general>
228                    before we use as(., <Tsparse>)[...] anyway
229    
230            * R/Rsparse.R (.viaC.to.R): mostly instead of .viaC.to.dgR()
231    
232            * R/triangularMatrix.R (isTriangular): methods for all subclasses
233            instead of "triangularMatrix" -- just to disambiguate
234    
235    2008-02-14  Martin Maechler  <maechler@stat.math.ethz.ch>
236    
237            * tests/Class+Meth.R (dotestMat): add m[FALSE, FALSE] { <-> TODO}
238            * tests/indexing.R: example that fails above
239    
240    2008-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
241    
242            * R/Matrix.R (.M.sub.i.2col): fix for logical matrix indexing
243            * R/Tsparse.R (.TM.sub.i.2col, .TM.repl.i.2col): ditto;
244                    now, M[lower.tri(M)] and  M[lower.tri(M)] <- v  work better
245    
246            * src/Tsparse.c (Tsparse_to_tCsparse): new fast utility.
247            * src/Tsparse.h, init.c: ditto
248            * R/Auxiliaries.R (isTriT): new; faster than going via Csparse
249                 both isTriC() and isTriT() now return TRUE with "kind" or FALSE.
250            * R/sparseMatrix.R (isTriangular): hence simplified
251    
252    2008-01-24  Martin Maechler  <maechler@stat.math.ethz.ch>
253    
254            * R/Ops.R (.Arith.Csparse): new utility factored out of former
255              <dgC> o <dgC>, extended for triangular and also used in  <dtC> o <dtC>.
256    
257    2008-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
258    
259            * tests/factorizing.R (checkSchur): and more tests for checking Schur()
260    
261            * inst/test-tools.R (isOrthogonal): new function; also file restructured
262    
263    2008-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
264    
265            * R/ngTMatrix.R: allow as(<numeric matrix>, "ngTMatrix") and hence
266            coercion to "nMatrix" and "pMatrix"
267    
268            * R/AllClass.R: "Schur" class;  "number" class union
269            * man/number-class.Rd:
270            * man/Schur-class.Rd:
271    
272            * R/eigen.R (.dgeSchur): utility, and return "Schur" class
273            (.simpleSchur): Schur() method for diagonal matrices
274            (.triSchur):    Schur() method for triangular matrices
275            (Schur.sym):    Schur() for symmetric matrices {building on eigen()}.
276    
277    
278    2008-01-21  Martin Maechler  <maechler@stat.math.ethz.ch>
279    
280            * src/dgCMatrix.c (dgCMatrix_QR): set @Dim slot (as per doc)
281    
282    2008-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
283    
284            * R/CHMfactor.R (solve): method for b="numeric", but also b="ANY"
285                    in order to ensure 'system = *' is not lost;
286                    formals()$system instead of cut&paste.
287            * tests/factorizing.R: test solve(<CHM..>, <numeric>)
288    
289    2008-01-11  Martin Maechler  <maechler@stat.math.ethz.ch>
290    
291            * DESCRIPTION (Date): make ready for release --> 0.999375-4
292    
293            * R/dgeMatrix.R: fix rcond() method for "dgeMatrix".
294    
295    2007-12-08  Martin Maechler  <maechler@stat.math.ethz.ch>
296    
297            * R/pMatrix.R: as(*, "matrix") now returns 0/1 *integer* matrix,
298                    and hence does as.vector(.).
299            * man/pMatrix-class.Rd: docs
300            * R/sparseMatrix.R: fix for printing "integer sparse"
301    
302            * tests/Class+Meth.R (tstMatrixClass): test M[FALSE], M[2] etc
303    
304            * R/Matrix.R and others: use "exact" function argument list for
305                    both "["   : (x, i,j, ..., drop)
306                    and  "[<-" : (x, i,j, ..., value)
307    
308            * R/denseMatrix.R: M[i] and M[i] <- v  (i vector) now work
309            * R/Tsparse.R (replTmat):    ditto
310            * R/diagMatrix.R (replDiag): ditto
311            * R/Csparse.R (replCmat):    ditto {was it worth the pain?}
312            * tests/indexing.R: testing the above
313    
314    2007-12-07  Martin Maechler  <maechler@stat.math.ethz.ch>
315    
316            * R/sparseMatrix.R (cov2cor): method for sparse matrices
317    
318            * R/diagMatrix.R ([<-): fix   D[ cbind(i,j) ] <- v
319    
320            * R/bind2.R: fix for Rsparse* and rbind2(dense,dense)
321    
322            * tests/Class+Meth.R: test cbind2, rbind2  and  diag<-
323    
324    2007-12-06  Martin Maechler  <maechler@stat.math.ethz.ch>
325    
326            * R/Matrix.R: "generic" cov2cor() method
327    
328            * R/nearPD.R: new 'only.values', 'keepDiag' arguments;
329                    speed up Q %*% D %*% t(Q)
330            * tests/dpoMatrix.R: test nearPD()
331    
332    2007-12-05  Doug Bates and Martin Maechler
333    
334            * R/sparseMatrix.R: xtabs(*, sparse=.) function; an extention of
335            stats::xtabs() allowing to create sparse matrices.
336    
337    2007-10-08  Martin Maechler  <maechler@stat.math.ethz.ch>
338    
339            * DESCRIPTION (Version): *-4 (released *-3 two days ago)
340    
341    2007-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
342    
343            * R/pMatrix.R: solve(<Matrix>, <pMatrix>)
344    
345    2007-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
346    
347            * R/LU.R: solve() method for "denseLU"
348    
349    2007-10-01  Martin Maechler  <maechler@stat.math.ethz.ch>
350    
351            * DESCRIPTION (Version): 0.999375-3 preparing for release
352    
353            * R/AllGeneric.R: simplify  if(.) .. else .. for R <= 2.5.1
354    
355            * R/Matrix.R (Matrix): .Internal(matrix(..)) different for R >= 2.7.0
356    
357    2007-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
358    
359            * R/pMatrix.R (.m.mult.pMat): fix <matrix> %*% <pMatrix>,
360              thanks to Kasper Kristensen.
361            * tests/matprod.R: regression test for that.
362    
363    2007-09-23 17:32  Douglas Bates <bates@stat.wisc.edu>
364    
365            * [r4778] R/AllGeneric.R: Check R version before defining generics for
366              primitives
367    
368    2007-09-13  Martin Maechler  <maechler@stat.math.ethz.ch>
369    
370            * R/denseMatrix.R (rcond): method
371            * R/sparseQR.R (rcond): method, use x or t(x)
372    
373    2007-09-12  Martin Maechler  <maechler@stat.math.ethz.ch>
374    
375            * R/dgeMatrix.R (rcond): method: work via qr.R() for non-square
376            matrices.
377            * R/sparseMatrix.R: Ditto for all other rcond() method definitions.
378    
379            * man/rcond.Rd: mention the more general definition, and add
380            example for non-square matrices.
381    
382            * man/chol.Rd: new file, for the S4 chol() generic and all methods.
383    
384    2007-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
385    
386            * R/sparseQR.R: add qr.R() method [to be used for rcond()]
387    
388    2007-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
389    
390            * R/Matrix.R ([<-): add (Matrix,missing,ANY,Matrix) etc
391            * tests/indexing.R: add new regression for the above cases.
392    
393    2007-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
394    
395            * src/Mutils.h (__sun): clause for alloca.h on Solaris
396    
397    2007-08-16  Martin Maechler  <maechler@stat.math.ethz.ch>
398    
399            * DESCRIPTION (Date, Version): 0.999375-2
400    
401    2007-08-15  Martin Maechler  <maechler@stat.math.ethz.ch>
402    
403            * R/HBMM.R (readMM): make work for pattern matrices as well
404    
405    2007-08-14 13:07  Douglas Bates <bates@stat.wisc.edu>
406    
407            * [r4730] src/Mutils.h: declare alloca
408            * [r4734] NAMESPACE, R/AllGeneric.R, R/Csparse.R, R/HBMM.R, R/Tsparse.R,
409              R/dgCMatrix.R, R/dgTMatrix.R, R/dsCMatrix.R, R/dsTMatrix.R,
410              man/externalFormats.Rd, src/Csparse.c, src/Csparse.h, src/DEPS.mkf,
411              src/HBMM.c, src/HBMM.h, src/Mutils.h, src/SOURCES_C.mkf, src/init.c,
412              src/mmio.c, src/mmio.h: Remove deprecated function writeHB and its
413              methods; switch writeMM to use CHOLMOD code; repair readMM
414    
415    2007-08-14  Martin Maechler  <maechler@stat.math.ethz.ch>
416    
417            * R/nearPD.R, man/nearPD.Rd (nearPD): new function built on Jens
418            Oehlschlaegel's ... result type still to be discussed!
419    
420    2007-08-10  Martin Maechler  <maechler@stat.math.ethz.ch>
421    
422            * man/image-methods.Rd: new, combining all image() methods
423    
424    2007-08-09  Martin Maechler  <maechler@stat.math.ethz.ch>
425    
426            * R/dgCMatrix.R: define qr() and lu() methods for "sparseMatrix"
427            to work via dgC...
428    
429            * R/Matrix.R (Matrix): special treatment for "table" (S3)
430    
431    2007-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
432    
433            * R/dgTMatrix.R (image): change defaults to
434                    aspect = "iso", colorkey = FALSE
435    
436    2007-08-06  Martin Maechler  <maechler@stat.math.ethz.ch>
437    
438            * src/dsyMatrix.c (dsyMatrix_matrix_mm): 'b' might be matrix;
439            must copy its *expanded* x slot before LAPACK call.
440    
441            * tests/matprod.R: test the last days' changes.
442    
443    2007-08-06 16:43  Douglas Bates <bates@stat.wisc.edu>
444    
445            * [r4712] inst/include/Matrix_stubs.c: Change R_cholmod_printf in stubs
446              as well as in sources
447            * [r4713] src/dsyMatrix.c: Duplicate the contents of the RHS before
448              Lapack call
449    
450    2007-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
451    
452            * R/Matrix.R (%*%, crossprod, tcrossprod): add method for
453                    ("Matrix", "matrix") which is needed in some cases.
454            Ditto for solve().
455    
456            * R/colSums.R (.as.dge.Fun): need ddenseMatrix methods to avoid
457            infinite recursion in dispatch for some cases.
458    
459    2007-08-02 08:48  Martin Maechler <maechler@stat.math.ethz.ch>
460    
461            * [r4693] src/chm_common.c: R_cholmod_printf() instead of Rprintf() just
462              so pointers match
463    
464    2007-08-02  Martin Maechler  <maechler@stat.math.ethz.ch>
465    
466            * DESCRIPTION (Date): set ready for release -- 0.999375-1
467    
468    2007-08-01 15:44  Douglas Bates <bates@stat.wisc.edu>
469    
470            * [r4686] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
471              src/chm_common.c, src/chm_common.h: Change API for
472              numeric_as_chm_dense and N_AS_CHM_DN
473    
474    2007-08-01  Martin Maechler  <maechler@stat.math.ethz.ch>
475    
476            * src/dtrMatrix.c (dtrMatrix_matrix_mm): fix dimensionality check (!)
477            * tests/matprod.R: regr.test for it
478    
479    2007-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
480    
481            * R/dMatrix.R: fix from Brian for   Math2(., digits = "missing")
482            * tests/group-methods.R: and regression-test it
483    
484    2007-07-19 19:45  Douglas Bates <bates@stat.wisc.edu>
485    
486            * [r4642] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
487              inst/include/cholmod.h, src/chm_common.c, src/init.c: Export
488              triplet_to_sparse, documentation, use typedefs
489    
490    2007-07-18  Martin Maechler  <maechler@stat.math.ethz.ch>
491    
492            * man/dpoMatrix-class.Rd: added 'corMatrix' example
493    
494            * src/dsyMatrix.[ch] (dsyMatrix_as_matrix): new 'keep_dimnames' arg
495            * src/dtrMatrix.[ch] (dtrMatrix_as_matrix): ditto
496            * src/init.c, R/dsyMatrix.R, R/dtrMatrix.R, R/lgTMatrix.R: ditto
497    
498            * R/lsparseMatrix.R: bug fix in "all" method
499            * R/Ops.R (.do.Logic.lsparse): "|" bug in borderline case
500    
501            * R/dsyMatrix.R (coerce->dsTMatrix): (i,j) slots should *not* have names
502            * R/ngTMatrix.R (coerce->ngTMatrix): ditto;
503                    + matrix |-> nMatrix coercion
504            * R/pMatrix.R: + setAs()  to dMatrix and from nMatrix
505            * man/pMatrix-class.Rd: ditto
506    
507            * R/Matrix.R (Summary): method for non-dMatrix
508    
509            * tests/Class+Meth.R (extraValid): new check about "dirty" slots
510            * tests/Class+Meth.R (tstMatrixClass): test norm(.);
511                    test all Summary methods.
512    
513    2007-07-16  Martin Maechler  <maechler@stat.math.ethz.ch>
514    
515            * R/dgeMatrix.R (norm, rcond): methods for 'matrix'
516    
517    2007-07-14  Martin Maechler  <maechler@stat.math.ethz.ch>
518    
519            * R/sparseMatrix.R (norm): simple methods for sparseMatrix
520    
521            * R/pMatrix.R (t?crossprod): methods for pMatrix
522    
523    2007-07-10  Douglas Bates  <bates@stat.wisc.edu>
524    
525            * src/dgeMatrix.c (dgeMatrix_colsums): Get the logic straight.
526    
527    2007-07-09 20:45  Douglas Bates <bates@stat.wisc.edu>
528    
529            * [r4579] src/dgeMatrix.c: Untangle horrible code in dgeMatrix_colsums
530              trying to fix a subtle bug - which has been somewhere else.
531    
532    2007-07-09 19:43  Martin Maechler <maechler@stat.math.ethz.ch>
533    
534            * [r4578] src/dgeMatrix.c: "cleaned" dgeMatrix_colsums() - but did not
535              solve the bug
536    
537    2007-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
538    
539            * src/dgCMatrix.c (compressed_to_TMatrix):
540    
541    2007-07-07  Martin Maechler  <maechler@stat.math.ethz.ch>
542    
543            * src/Csparse.c (Rsparse_validate): new, to have some validity
544            checking for RsparseMatrix
545            * src/dgCMatrix.c (xRMatrix_validate): ditto
546            * src/dtCMatrix.c (tRMatrix_validate): ditto
547    
548    2007-07-07  Douglas Bates <bates@stat.wisc.edu>
549    
550            * [r4567] R/AllClass.R: Slots already in RsparseMatrix were redefined in
551              lgRMatrix
552            * [r4568] DESCRIPTION: Prepare for bug-fix release
553            * [r4570] src/CHOLMOD/Check/cholmod_write.c: Include cholmod_matrixops.h
554              for declaration of cholmod_symmetry
555    
556    2007-07-06  Martin Maechler  <maechler@stat.math.ethz.ch>
557    
558            * DESCRIPTION (Version): 0.999375 merged into the trunk; ready for
559            release.
560    
561    2007-07-06 14:11  Douglas Bates <bates@stat.wisc.edu>
562    
563            * [r4559] src/iohb.c, src/iohb.h: Remove Harwell-Boeing input/output
564              functions - no longer used
565            * [r4560] src/HBMM.c, src/Mutils.c, src/dgTMatrix.c, src/dgeMatrix.c,
566              src/dspMatrix.c, src/dsyMatrix.c, src/dtCMatrix.c,
567              src/factorizations.c, src/sparseQR.c: Replace most calls to Calloc by
568              Alloca
569    
570    2007-07-06 13:14  Martin Maechler <maechler@stat.math.ethz.ch>
571    
572            * [r4558] inst/doc/Comparisons.Rnw, src/CHMfactor.c, src/Csparse.c,
573              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dense.c,
574              src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c, src/sparseQR.c,
575              src/t_gCMatrix_colSums.c: more R_CheckStack()s
576    
577    2007-07-05 18:12  Douglas Bates <bates@stat.wisc.edu>
578    
579            * [r4550] inst/include/Matrix.h: Add the macro N_AS_CHM_DN to "alloca"
580              the required amount of memory then call M_numeric_as_chm_dense.
581            * [r4556] src/Mutils.h, src/dgCMatrix.c: Define and use the Alloca macro
582              (like Calloc but calling alloca)
583    
584    2007-07-05  Martin Maechler  <maechler@stat.math.ethz.ch>
585    
586            * R/sparseMatrix.R (printSpMatrix): renamed from prSpMatrix()
587            and extended with more sophisticated 'col.names' option.
588            * NAMESPACE: export  printSparseMatrix()
589            * man/printSpMatrix.Rd: document, incl. examples
590    
591    2007-07-04 16:21  Douglas Bates <bates@stat.wisc.edu>
592    
593            * [r4543] src/cs_utils.c, src/cs_utils.h, src/dgCMatrix.c,
594              src/dtCMatrix.c, src/sparseQR.c: CSP typedef for *cs and macro
595              AS_CSP. API change - pass the empty structure to Matrix_as_cs.
596    
597    2007-07-04  Martin Maechler  <maechler@stat.math.ethz.ch>
598    
599            * DESCRIPTION (Version): 0.99875-4
600    
601            * tests/Class+Meth.R (tstMatrixClass): add dimnames, and hence test
602            some dimnames perservation.
603    
604            * R/dsTMatrix.R (t-method): keep dimnames
605            * R/dtTMatrix.R:  ditto
606    
607            * R/sparseMatrix.R (prSpMatrix): print colnames when non-trivial
608            and ncol(.) < 10
609    
610            * src/cs_utils.c: drop check_class() and use Matrix_check_class()
611            from Mutils.h
612    
613            * src/lgCMatrix.c ([ln]csc_to_matrix): no longer lose dimnames,
614            e.g. in as(<ngCMatrix>, "matrix")
615    
616    2007-07-01 13:27  Douglas Bates <bates@stat.wisc.edu>
617    
618            * [r4529] .: Create a branch for the API changes from the 0.99875
619              series to the 0.999375 series
620            * [r4530] DESCRIPTION, inst/include/Matrix.h,
621              inst/include/Matrix_stubs.c, src/CHMfactor.c, src/Csparse.c,
622              src/Mutils.h, src/Tsparse.c, src/chm_common.c, src/chm_common.h,
623              src/dense.c, src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c,
624              src/t_gCMatrix_colSums.c: API change - pass the empty structure to the
625              as_cholmod_x functions
626    
627    2007-06-30 09:05  Martin Maechler <maechler@stat.math.ethz.ch>
628    
629            * [r4527] trunk/Matrix/DESCRIPTION, trunk/Matrix/NAMESPACE,
630              trunk/Matrix/inst/doc/Comparisons.Rnw: add session- and hardware-info
631              to Comparisons
632    
633    >>>>>>> .merge-right.r4561
634    2007-06-29  Martin Maechler  <maechler@stat.math.ethz.ch>
635    
636            * DESCRIPTION (Version): 0.99875-3 ready to be released.
637    
638            * R/sparseMatrix.R (spMatrix): make spMatrix(3,4) working
639    
640            * R/AllGeneric.R: set "Math" (and "Math2") group generics in a way
641            that should also work in a future version of R.
642    
643    2007-06-21  Martin Maechler  <maechler@stat.math.ethz.ch>
644    
645            * NAMESPACE, R/AllClass.R: "xsparseVector" class union.
646    
647            * R/sparseVector.R: more *sparseVector coercions, notably for
648            non - double ones.
649    
650    2007-06-19  Martin Maechler  <maechler@stat.math.ethz.ch>
651    
652            * R/colSums.R: new file for all (col|row)(Sums|Means) methods,
653              notably the new ones building on the new .Call(.)s:
654    
655            * src/dgCMatrix.c (DEF_gCMatrix_COLSUMS): use to define
656            all 4 of [dlin]gCMatrix_colSums().
657    
658    2007-06-18 16:12  Douglas Bates <bates@stat.wisc.edu>
659    
660            * [r4472] src/Syms.h, src/init.c: Added Matrix_lengthSym
661            * [r4473] src/dgCMatrix.c: Modified dgCMatrix_colSums for sparseVector
662              result
663    
664    2007-06-16  Martin Maechler  <maechler@stat.math.ethz.ch>
665    
666            * R/kronecker.R: fix typo (could lead to inf.recursion)
667            * test/simple.R: testing that
668    
669            * R/sparseMatrix.R (prSpMatrix): change to be used as print()
670            method as well (which can have arguments, show() can't).
671    
672    2007-06-16 15:52  Douglas Bates <bates@stat.wisc.edu>
673    
674            * [r4466] R/dgCMatrix.R, src/dgCMatrix.c, src/dgCMatrix.h, src/init.c:
675              added dgCMatrix_colSums for [col,row][Sums,Means]
676    
677    2007-06-15 23:15  Douglas Bates <bates@stat.wisc.edu>
678    
679            * [r4460] R/sparseMatrix.R, man/dgCMatrix-class.Rd, src/dgCMatrix.c,
680              src/dgCMatrix.h, src/init.c: added lm.fit.sparse (unexported),
681              coercion of "factor" to "dgCMatrix" and dgCMatrix_cholsol
682            * [r4461] R/AllClass.R, man/sparseMatrix-class.Rd: draft "indicators"
683              class
684            * [r4463] R/sparseMatrix.R, man/dgCMatrix-class.Rd,
685              man/sparseMatrix-class.Rd: Don't need an "indicators" class - use the
686              row names to store the levels - duh!  Added an example.
687    
688    2007-06-14  Martin Maechler  <maechler@stat.math.ethz.ch>
689    
690            * src/Csparse.c (Csparse_validate): check for *repeated* entries
691            thanks to example from Christian Buchta; with a test here:
692            * tests/simple.R:
693    
694    2007-06-07  Martin Maechler  <maechler@stat.math.ethz.ch>
695    
696            * R/Auxiliaries.R (callGeneric): another fix, needed for some cases
697            of colSums(*, sparseResult = TRUE)
698    
699    2007-06-06  Martin Maechler  <maechler@stat.math.ethz.ch>
700    
701            * R/lsparseMatrix.R, R/ldenseMatrix.R (all, any): change default to
702            'na.rm = FALSE' as "everywhere" else in R.
703    
704    2007-06-05 Douglas Bates <bates@stat.wisc.edu>
705    
706            * [r4421] src/CSparse_install.sh: Modify for new organization of
707              CSparse package
708            * [r4425] src/UFsparse_download.sh: Update to version 3.0.0 of
709              SuiteSparse
710            * [r4426] src/Makefile: add ./UFconfig to the include path for
711              compilation
712            * [r4427] src/cs.[ch]: update to CSparse version 2.2.0
713            * [r4428] inst/doc/UFsparse/* src/{AMD,CHOLMOD,COLAMD}/*
714              src/UFconfig/UFconfig.h: Update to version 3.0.0 of SuiteSparse
715    
716    2007-06-05  Martin Maechler  <maechler@stat.math.ethz.ch>
717    
718            * R/Auxiliaries.R (emptyColnames): + argument msg.if.not.empty, used in
719            * R/sparseMatrix.R (prSpMatrix): now gives a message about
720            suppressed column names.
721    
722    2007-06-04 17:13  Douglas Bates <bates@stat.wisc.edu>
723    
724            * [r4418] src/Csparse.c, src/HBMM.c, src/Mutils.c, src/Mutils.h,
725              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dgCMatrix.c,
726              src/dgeMatrix.c, src/dpoMatrix.c, src/dpoMatrix.h, src/dppMatrix.c,
727              src/dppMatrix.h, src/dsCMatrix.c, src/dspMatrix.c, src/dspMatrix.h,
728              src/dsyMatrix.c, src/dsyMatrix.h, src/dtpMatrix.c, src/dtrMatrix.c:
729              Remove warnings after change to const char* CHAR
730    
731    2007-06-04 17:11  Douglas Bates <bates@stat.wisc.edu>
732    
733            * [r4417] inst/include/Matrix_stubs.c, inst/include/cholmod.h: Corrected
734              type of M_cholmod_ssmult
735    
736    2007-06-03 14:42  Douglas Bates <bates@stat.wisc.edu>
737    
738            * [r4412] inst/include/Matrix_stubs.c, inst/include/cholmod.h,
739              src/init.c: Yet another cholmod export - cholmod_ssmult
740    
741    2007-05-23  Martin Maechler  <maechler@stat.math.ethz.ch>
742    
743            * NAMESPACE: exported drop0(), since
744            * man/drop0.Rd: I have seen several cases, I really wanted to use
745            it, so our users may want too.
746    
747    2007-05-22  Martin Maechler  <maechler@stat.math.ethz.ch>
748    
749            * man/colSums.Rd: separately document colSums() etc, since these
750            have the extra argument 'sparseResult'.
751    
752    2007-05-21  Martin Maechler  <maechler@stat.math.ethz.ch>
753    
754            * R/sparseMatrix.R (spMatrix): utility (T)sparse Matrix constructor;
755            * man/spMatrix.Rd: docu., including examples
756    
757            * R/Auxiliaries.R (sp.colMeans): etc, using a patched callGeneric(),
758            in order to make colMeans() etc fast *and* correct.
759            * R/sparseVector.R (replSPvec): "[<-" functionality for
760            sparseVectors; tested in
761            * tests/simple.R:
762    
763    2007-05-19  Martin Maechler  <maechler@stat.math.ethz.ch>
764    
765            * R/sparseMatrix.R (print.sparseSummary): and summary() method for
766            (very) sparse Matrices; output similar to Matlab's print().
767    
768    2007-05-17  Douglas Bates  <bates@stat.wisc.edu>
769    
770            * src/HBMM.c (Matrix_writeMatrixMarket): Write 1-based, not
771            0-based, indices (Jose Quesada <quesada@gmail.com>).
772    
773    2007-05-16  Douglas Bates  <bates@stat.wisc.edu>
774    
775            * R/CHMfactor.R: Added solve methods for a CHMfactor object.
776    
777    2007-05-16  Martin Maechler  <maechler@stat.math.ethz.ch>
778    
779            * R/Auxiliaries.R (sparsapply): new utility, much faster than
780            tapply1() for large sparse matrices.
781    
782    2007-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
783    
784            * R/Matrix.R (dim<-): reshape now via sparseVector.
785    
786            * R/sparseVector.R: methods and function for
787            * R/AllClass.R: new "sparseVector" class and daughters.
788            * NAMESPACE: export new classes
789    
790    2007-05-14  Martin Maechler  <maechler@stat.math.ethz.ch>
791    
792            * DESCRIPTION (Version): 0.99875-1
793            * src/Makefile.win: also remove Lapack code from here (cf. 04-25).
794    
795    2007-05-11  Martin Maechler  <maechler@stat.math.ethz.ch>
796    
797            * R/Tsparse.R ([, Tsparse): fix last case: *duplicated*, symmetric
798            indexing
799            * tests/indexing.R: test set for that.
800    
801    2007-05-08  Martin Maechler  <maechler@stat.math.ethz.ch>
802    
803            * R/Tsparse.R (replTmat): fix the case of *duplicated* index
804            entries.
805            * tests/indexing.R(out): add regression test for it
806    
807    2007-04-30  Martin Maechler  <maechler@stat.math.ethz.ch>
808    
809            * R/(l(dense|sparse))?Matrix.R (!): use 'x', not 'e1' as argument
810            name for "!" method definitions.
811    
812    2007-04-26  Martin Maechler  <maechler@stat.math.ethz.ch>
813    
814            * R/Tsparse.R (intI): new utility, used for "[" :
815                    Cleanup up there, and fixes for duplicated indices - more TODO!
816    
817            * tests/indexing.R(out): more tests
818    
819    2007-04-25  Douglas Bates  <bates@stat.wisc.edu>
820    
821            * DESCRIPTION,src/Makefile: require R>= 2.5.0 and remove Lapack
822            code that is now part of the R Lapack library.
823    
824            * src/init.c,inst/include/{Matrix_stubs.c,cholmod.h}:export
825            cholmod_factorize_p (used in lme4 for GLMMs and NLMMs).
826    
827    2007-04-21  Martin Maechler  <maechler@stat.math.ethz.ch>
828    
829            * R/Matrix.R (image): method for all Matrices, not just sparse ones.
830    
831    2007-04-17  Martin Maechler  <maechler@stat.math.ethz.ch>
832    
833            * R/Auxiliaries.R (tapply1): unname(.) -> colSums() etc don't end
834            up with extraneous names '0'...'<n-1>'
835    
836    2007-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
837    
838            * R/dgTMatrix.R (mat2dgT): care about NAs
839    
840    2007-04-11  Martin Maechler  <maechler@stat.math.ethz.ch>
841    
842            * R/kronecker.R: triangularity preserving methods
843    
844    2007-03-27  Martin Maechler  <maechler@stat.math.ethz.ch>
845    
846            * R/kronecker.R: new file collecting kronecker() methods in one
847                    place.  Goal: become much faster!
848    
849    2007-03-23  Martin Maechler  <maechler@stat.math.ethz.ch>
850    
851            * src/dtCMatrix.c (dtCMatrix_solve): use the new code from Kasper
852            Kristensen based cs_spsolve() instead of _lsolve & _usolve which
853            can be much faster.
854    
855            * tests/matprod.R: add regression tests for these (upper & lower).
856    
857    2007-03-19  Martin Maechler  <maechler@stat.math.ethz.ch>
858    
859            * R/Matrix.R (diff): method for our Matrices.
860    
861            * R/sparseMatrix.R (isDiagonal): check dim()!
862    
863    2007-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
864    
865            * R/Matrix.R (dim<-): new method for "reshape()" built on a
866            proposal from Tamas Papp.
867    
868    2007-03-16  Martin Maechler  <maechler@stat.math.ethz.ch>
869    
870            * R/AllGeneric.R: remove all  if(!isGeneric(.))  clauses
871    
872            * R/zzz.R (.onLoad, .onUnload): do *not* leave bind_activation(TRUE);
873            rather define and export  cBind() and rBind() only.
874            --> useRs *must* change code that used to have cbind()/rbind() !!
875    
876            * R/bind.R: change tests from cbind() to cBind() and similarly to rBind()
877            * R/bind.Rout.save: ditto
878    
879    2007-02-16  Douglas Bates  <bates@r-project.org>
880    
881            * DESCRIPTION (Date, Version): 0.9975-11 with new date
882            * src/dgCMatrix.c (R_to_CMatrix, compressed_to_TMatrix): remove
883            const modifier on declaration of the array 'valid'
884    
885    2007-02-12  Douglas Bates  <bates@stat.wisc.edu>
886    
887            * R/CHMfactor.R: Add image method (coercion to sparseMatrix).
888    
889    2007-02-05  Martin Maechler  <maechler@stat.math.ethz.ch>
890    
891            * DESCRIPTION (Date, Version): 0.9975-10 with new date.
892    
893            * R/Ops.R (Arith): make sure Csparse o Csparse also works for e.g. ntCMatrix
894            * tests/simple.R: test the above and some of these coercions:
895    
896            * R/nsparseMatrix.R: coercing "Csparse" to "lsparseMatrix";
897                    be careful to avoid infinite recursion, using new coercions in
898            * R/ngCMatrix.R and nsC... and ntC...
899            * R/lsparseMatrix.R: ditto
900    
901            * R/SparseM-conv.R: more conversion, notably for triplet matrices.
902    
903            * src/dgCMatrix.c (R_to_C_Matrix): port Doug's fix and
904            * R/Rsparse.R: reactivate .Call()s
905    
906            * tests/Class+Meth.R: a bit more on actual classes
907    
908    2007-02-04  Douglas Bates  <bates@stat.wisc.edu>
909    
910            * src/dgCMatrix.c (compressed_to_TMatrix): fix memory bug using strdup()
911    
912    2007-02-03  Martin Maechler  <maechler@stat.math.ethz.ch>
913    
914            * DESCRIPTION (Version): 0.9975-10 to upload
915    
916            * tests/Class+Meth.R (tstMatrixClass): require coercions to
917            specific classes less unconditionally.
918    
919            * R/Auxiliaries.R: get rid of as_Tsparse() and as_Rsparse()
920    
921            * R/Tsparse.R (triu): etc, use as(*, "TsparseMatrix") instead of as_Tsparse()
922    
923            * R/Rsparse.R (.R.2.T): R-level workaround using compressed_to_TMatrix.
924            * R/Rsparse.R (.R.2.C): R-level workaround since C-level
925            R_to_CMatrix segfaults on one platform.
926            Eliminate most coercion method to *specific* classes, and replace
927            with virtual classes coercions.
928    
929    
930    2007-02-01  Martin Maechler <maechler@stat.math.ethz.ch>
931    
932            * src/init.c: export the CHM...._validate() placeholders, since
933            they *are* called.
934    
935            * tests/Class+Meth.R (classCanCoerce): and starting to test
936            all as(<from>, <to>)
937    
938    2007-01-30  Martin Maechler  <maechler@stat.math.ethz.ch>
939    
940            * R/Tsparse.R ([): more care when subsetting triangular Tsparse
941            * tests/indexing.R: tested now
942            * tests/indexing.Rout.save: updated
943    
944            * src/Csparse.c (Csparse_to_dense): use Rkind = -1 for PATTERN to
945            * src/chm_common.c (chm_dense_to_SEXP): return "ngeMatrix" when
946            appropriate.
947    
948            * NAMESPACE: export a trivial
949            * R/Matrix.R: drop() Matrix-method
950    
951            * R/AllClass.R: moved all prototypes to virtual super classes.
952    
953            * R/Rsparse.R: many more coercions to have less exceptions in
954            * tests/Class+Meth.R:
955    
956            * R/Ops.R (Compare): tweak for case with NA
957            * tests/simpl.R: hence another 'FIXME' eliminated
958    
959    2007-01-29  Martin Maechler  <maechler@stat.math.ethz.ch>
960    
961            * R/diagMatrix.R (solve): the obvious methods for diagonalMatrix
962            objects.
963    
964            * tests/Class+Meth.R (tstMatrixClass): now testing diag(), nnzero(),
965              and more of "!", "&", "|", all, any; coercions
966    
967            * R/Rsparse.R: many coercions (which enable quite a few other
968            methods), thanks to enhancements in
969            * src/dgCMatrix.c (R_to_CMatrix): new, and
970            * src/dgCMatrix.c (compressed_to_TMatrix): now for (d,l,n) ,
971            symmetric & triangular and ..RMatrix objects.
972    
973            * src/TMatrix_as.c (Matrix_T_as_DENSE,Matrix_T_as_GENERAL):
974            renamed file from src/dsTMatrix.c;
975            now dealing with symmetric and triangular Tsparse coercions, both
976            to dense and general.
977    
978    2007-01-27  Martin Maechler  <maechler@stat.math.ethz.ch>
979    
980            * src/dsTMatrix.c: has now "l" and "n" methods besides the "d" ones.
981    
982            * R/Ops.R (Arith): <dgCMatrix> o <numeric> now remains sparse
983            where sensible when the <numeric> is of length > 1.
984    
985    2007-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
986    
987            * R/Matrix.R ([<-): for M[] <- value: fix length
988    
989    2007-01-25  Martin Maechler  <maechler@stat.math.ethz.ch>
990    
991            * R/Auxiliaries.R (n2l_Matrix): new, to be used in
992            * R/ndenseMatrix.R: new coercions n* -> l*
993    
994    2007-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
995    
996            * R/triangularMatrix.R: new file; simple triu() and tril() methods.
997    
998            * R/Ops.R ("Logic"): and other "Ops", many updates
999    
1000    2007-01-18  Martin Maechler  <maechler@stat.math.ethz.ch>
1001    
1002            * src/Mutils.h (SET_DimNames): new utility
1003    
1004            * R/Auxiliaries.R (nnzero): improved and now exported via
1005    
1006            * NAMESPACE: + nnzero(); length() == prod(dim(.)) method for all "Matrix" objects
1007    
1008    2007-01-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1009    
1010            * R/diagMatrix.R (!): fix typo.
1011    
1012    2007-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
1013    
1014            * R/Auxiliaries.R (as_Csparse): and quite a few others:
1015                    allow to pass class definition --> speedup
1016            * R/sparseMatrix.R: apply the above
1017    
1018            * R/Csparse.R: coercion Csparse* to dense* now preserves shape properties.
1019    
1020            * src/Mutils.h (mMatrix_as_geMatrix): new, based on
1021            * src/Mutils.c (dup_mMatrix_as_geMatrix): new; generalization of
1022            old dup_mMatrix_as_dgeMatrix), eliminating a long-standing "FIXME".
1023    
1024            * src/dense.c (dense_to_Csparse): use new mMatrix_as_geMatrix()
1025    
1026            * R/denseMatrix.R (.dense2C): based on dense_to_Csparse: name it,
1027            and use it for "sparse*" as well, since it's faster than the
1028            as_Csparse(.) way.
1029    
1030    2007-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
1031    
1032            * R/Ops.R ("Logic"): more methods, notably an  <lgC> o <lgC> one.
1033    
1034    2007-01-12  Martin Maechler  <maechler@stat.math.ethz.ch>
1035    
1036            * R/Tsparse.R (.TM.repl.i.2col): new internal function to be used
1037            as method for   M[ ij ] <- v
1038            * R/Csparse.R:: go via Tsparse for "M[ij] <- v"
1039    
1040            * R/Ops.R: "Compare" for (C|R)sparse: need pointer slot for all
1041            FALSE answer
1042    
1043            * R/Csparse.R (replCmat): fix the "all non-zero" case with reordering
1044            * tests/indexing.R: test it, and some of the above
1045    
1046    2007-01-05  Martin Maechler  <maechler@stat.math.ethz.ch>
1047    
1048            * R/Auxiliaries.R (is_duplicatedT): new utility
1049    
1050    2007-01-05  Douglas Bates  <bates@stat.wisc.edu>
1051    
1052            * src/init.c (R_init_Matrix): export cholmod_scale
1053    
1054    2006-12-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1055    
1056            * R/zzz.R (tmp): for R >= 2.5.0, extend formals of our
1057            base::as.matrix to (x, ...)
1058    
1059    2006-12-28  Martin Maechler  <maechler@stat.math.ethz.ch>
1060    
1061            * R/Ops.R ("Arith" etc): move almost all "Ops" methods to new R
1062            file; start using "Logic", hence
1063    
1064            * DESCRIPTION (Depends): R >= 2.4.1 (since we want "Logic")
1065            * NAMESPACE: import and export "Logic"
1066    
1067    2006-12-27  Martin Maechler  <maechler@stat.math.ethz.ch>
1068    
1069            * src/zpotfr.f and dependencies: use LAPACK 3.1 version
1070            only needed previously to R version 2.5.0.
1071    
1072    2006-12-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1073    
1074            * DESCRIPTION (Date, Version): 0.9975-8, ready for release
1075    
1076            * R/Tsparse.R (replTmat): fix subassignment of triangular
1077            * R/Csparse.R (replCmat): ditto
1078            * tests/indexing.R: more tests, incl the above fix
1079    
1080    2006-12-23  Martin Maechler  <maechler@stat.math.ethz.ch>
1081    
1082            * R/Auxiliaries.R (drop0): extend for non CSparse
1083            * R/Auxiliaries.R (diagU2N): should work for all sparseMatrix
1084    
1085            * src/Csparse.c (Csparse_to_Tsparse, Csparse_general_to_symmetric):
1086                    use uplo correctly (!); other places: use uplo_P() macro
1087    
1088            * R/Csparse.R (replCmat): call diagU2N() when needed
1089            * R/Tsparse.R (replTmat): ditto
1090    
1091            * src/dtCMatrix.c (tCMatrix_validate): new
1092            * src/dtTMatrix.c (tTMatrix_validate): new, used in
1093            * R/AllClass.R: for validity of dtC, dsC, and dtT, dsT.
1094    
1095            * R/diagMatrix.R (replDiag): to use in [<-
1096    
1097    2006-12-22  Martin Maechler  <maechler@stat.math.ethz.ch>
1098    
1099            * R/Auxiliaries.R (as_Csparse2, as_geSimpl): new functions;
1100                    also more general diagU2N().
1101    
1102    2006-12-21  Martin Maechler  <maechler@stat.math.ethz.ch>
1103    
1104            * R/bind2.R: new file for all cbind2(), rbind() methods moved here
1105            from R/<foo>Matrix.R files. Better diagonal & improved sparse methods.
1106    
1107    2006-12-20  Martin Maechler  <maechler@stat.math.ethz.ch>
1108    
1109            * tests/bind.R: a few more cases
1110            * R/Auxiliaries.R (.M.kind): also work for atomic vectors
1111    
1112            * R/denseMatrix.R (cbind2/rbind2): moved here (and generalized) from
1113            * R/ddenseMatrix.R (cbind2/rbind2)
1114            * R/Tsparse.R (replTmat): final(?!) fix for "[<-" ..
1115            * tests/indexing.R
1116            * tests/indexing.Rout.save: updated
1117    
1118    2006-12-18  Martin Maechler  <maechler@stat.math.ethz.ch>
1119    
1120            * R/Tsparse.R (replTmat): fixed a remaining "[<-" bug in
1121            * tests/indexing.R
1122    
1123    2006-12-15  Martin Maechler  <maechler@stat.math.ethz.ch>
1124    
1125            * R/sparseMatrix.R (prSpMatrix): "." alignment much improved:
1126            align with proper position of "0", i.e., right for integers.
1127            argument 'align' by default is "fancy".
1128    
1129    2006-12-14  Martin Maechler  <maechler@stat.math.ethz.ch>
1130    
1131            * R/sparseMatrix.R: delegate "Compare" to "Csparse.."
1132            * R/Csparse.R: and fix "Compare" for more cases.
1133            * tests/Class+Meth.R: test some of these (m == m, m != m)
1134    
1135    2006-12-13  Martin Maechler  <maechler@stat.math.ethz.ch>
1136    
1137            * R/lsparseMatrix.R: all() and any() methods
1138            * R/ldenseMatrix.R:      ditto
1139            * NAMESPACE, R/Matrix.R: ditto
1140    
1141            * man/all-methods.Rd: document them minimally
1142    
1143            * tests/simple.R: add a few examples for these
1144    
1145    2006-12-11  Martin Maechler  <maechler@stat.math.ethz.ch>
1146    
1147            * R/Tsparse.R ([): fix long standing typo in symmetric case
1148            * man/dsCMatrix-class.Rd: add example exhibiting the above case
1149    
1150    2006-12-10  Douglas Bates  <bates@stat.wisc.edu>
1151    
1152            * src/CHMfactor.c (CHMfactor_to_sparse): change LDL factorization
1153            to LL before converting to a sparse matrix. (The LDL form can be
1154            converted to a sparse matrix but it is implicitly a unit
1155            triangular matrix and a diagonal matrix overwritten on the diagonal.)
1156    
1157    2006-12-09  Douglas Bates  <bates@stat.wisc.edu>
1158    
1159            * src/chm_common.c (chm_factor_to_SEXP): allocate and fill the Dim slot.
1160    
1161    2006-12-08  Douglas Bates  <bates@stat.wisc.edu>
1162    
1163            * DESCRIPTION (Version): updated -> release 0.9975-7
1164            * src/{init.c,chm_common.c}, inst/include/*: export cholmod_analyze_p
1165    
1166    2006-11-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1167    
1168            * R/diagMatrix.R (%*%): write a direct [diag o Csparse] method
1169    
1170    2006-11-29  Douglas Bates  <bates@stat.wisc.edu>
1171    
1172            * src/dgeMatrix.c (dgeMatrix_solve): Check error code from dgetri.
1173            * tests/dg_Matrix.R: Add Barry Rowlingson's test of a matrix that
1174            is exactly singular.
1175    
1176    2006-11-07  Martin Maechler  <maechler@stat.math.ethz.ch>
1177    
1178            * DESCRIPTION (Date): updated -> release 0.9975-6
1179    
1180    2006-11-06  Martin Maechler  <maechler@stat.math.ethz.ch>
1181    
1182            * R/Csparse.R (replCmat): symmetric indexing of symmetric matrix
1183            now returns symmetric.
1184    
1185            * R/zzz.R ("diag<-"): replace "diag<-" in base for R <= 2.4.x
1186    
1187            * R/Matrix.R (.M.sub.i.2col):  new, for  M[ cbind(i,j) ] indexing.
1188            * R/Matrix.R (.M.repl.i.2col): new, for  M[ cbind(i,j) ] <- value
1189    
1190            * R/Auxiliaries.R (.type.kind): added
1191    
1192    2006-11-04  Martin Maechler  <maechler@stat.math.ethz.ch>
1193    
1194            * src/cs.[ch]: updated to CSparse Version 2.0.3 by simply
1195            running src/CSparse_install.sh
1196    
1197            * R/denseMatrix.R: "[": keep symmetric on symmetric indexing.
1198    
1199    2006-11-03  Martin Maechler  <maechler@stat.math.ethz.ch>
1200    
1201            * src/dsCMatrix.c (dsCMatrix_Csparse_solve): new
1202            * R/dsCMatrix.R (solve): "fully-sparse" using the above.
1203    
1204            * R/AllClass.R: "pMatrix" now also inherits from "generalMatrix"
1205    
1206            * tests/Class+Meth.R (tstMatrixClass): now assure
1207            the (important in method programming) property :
1208    
1209                    ###>>  Every "Matrix" is either
1210                    ###>>  "general*", "symmetric*", "triangular*" or "diagonal*"
1211    
1212                    (where "*" stands for "Matrix")
1213    
1214            * R/Auxiliaries.R (diagU2N): now .Call()s Csparse_diagU2N for <Csparse>
1215    
1216            * R/dMatrix.R (Compare(<dMatrix>,<dMatrix>): update and
1217            * tests/validObj.R: checks for "comparison"
1218    
1219            * R/sparseMatrix.R ([): improved indexing for sparse;
1220                    trying to keep <symmetric>[ n, n] symmmetric
1221    
1222            * tests/indexing.R: indexing for logical sparse now ok
1223    
1224    
1225    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
1226    
1227            * src/Tsparse.c: use xTsparse_validate() , and hence remove
1228    
1229            * src/{ltC,lsC,lgT}Matrix.[ch]: removed
1230    
1231    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
1232    
1233            * R/AllClass.R (Matrix-class): check length of dimnames in validity.
1234    
1235            * tests/simple.R: validObject() checking the above.
1236    
1237            * src/dgCMatrix.c (xCMatrix_validate): new, small and simple,
1238            replacing both dgCMatrix_validate and lgCM*.
1239    
1240            * src/Csparse.c (Csparse_dense_prod, etc): do not lose dimnames;
1241            fix dimnames setting in other places.
1242            * src/chm_common.c (chm_dense_to_SEXP): now can pass dimnames
1243    
1244    2006-11-01  Martin Maechler  <maechler@stat.math.ethz.ch>
1245    
1246            * R/Csparse.R,src/Csparse.c, etc: tcrossprod(<CsparseM>,<CsparseM>)
1247    
1248            * R/sparseMatrix.R (isSymmetric): drop 'factors' slot for
1249            symmetry test, via
1250            * R/Auxiliaries.R (.as.dgC.0.factors):
1251    
1252    2006-11-01  Douglas Bates  <bates@r-project.org>
1253    
1254            * R/Csparse.R,src/Csparse.c,tests/matprod.R,
1255            man/CsparseMatrix-class.Rd: crossprod(<CsparseMatrix>,
1256            <CsparseMatrix>) added
1257    
1258    2006-10-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1259    
1260            * tests/matprod.R: add a variation of Harri's example
1261    
1262            * R/dsparseMatrix.R: fix crossprod(<dsparse>, <dge>) to *not*
1263            recursive infinitely.
1264    
1265            * R/dgCMatrix.R: + solve(<sparse>, <sparse>)
1266    
1267            * tests/indexing.R: add test for the "<" bug fixed 10-27 in R/dMatrix.R
1268    
1269    2006-10-28  Martin Maechler  <maechler@stat.math.ethz.ch>
1270    
1271            * tests/Class+Meth.R (tstMatrixClass): more: use non-trivial
1272            matrix if possible; test m+m == 2*m; now test dgRMatrix.
1273            * R/dgRMatrix.R (.to.dgR): a few more coercions, in order to
1274            satisfy the above test.
1275    
1276    2006-10-27  Martin Maechler  <maechler@stat.math.ethz.ch>
1277    
1278            * R/Matrix.R (Ops):  <Matrix> o <matrix>  method added
1279    
1280            * R/dgCMatrix.R: solve(a, b="missing") based on
1281            * src/dgCMatrix.c (dgCMatrix_matrix_solve): extend to work with
1282            RHS = NULL.
1283    
1284            * R/diagMatrix.R (diagdiagprod): extend %*% etc to ldiMatrix;
1285            add more (needed) [t]crossprod() methods.
1286    
1287            * man/ddiMatrix-class.Rd: more info, notably on 'diag'
1288    
1289            * R/Auxiliaries.R (as_CspClass): cleanup
1290            (drop0): internal utility for "Csparse_drop(*, 0)"
1291            (.bail.out.2): encourage active feedback
1292    
1293    2006-10-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1294    
1295            * R/dMatrix.R(Compare): new(), then slots [no validity check]
1296    
1297            * src/Csparse.c (Csparse_validate): fixed (and more efficient in
1298            non-valid or 'sorted' case).
1299    
1300            * R/dsparseMatrix.R: add "chol" method.
1301            * R/ddenseMatrix.R: ditto
1302    
1303            * R/diagMatrix.R (Ops): group methods for  <diagonal> o <sparse>
1304            * NAMESPACE (Ops)
1305            * R/diagMatrix.R (diag2T): simple utility used "higher level"
1306            coercion; deprecating direct lower level coercions.
1307    
1308            * R/*.R (seq): use seq_len() and seq_along() where possible.
1309    
1310    
1311    2006-10-23  Martin Maechler  <maechler@stat.math.ethz.ch>
1312    
1313            * DESCRIPTION (Version): 0.9975-5 ready for release
1314    
1315    2006-10-20  Douglas Bates  <bates@stat.wisc.edu>
1316    
1317            * src/init.c (R_init_Matrix): export more cholmod CCallable functions.
1318    
1319    2006-10-20  Martin Maechler  <maechler@stat.math.ethz.ch>
1320    
1321            * R/AllClass.R (corMatrix): add 'validity' check;
1322                    comment out unused "LDL" class definition
1323            * NAMESPACE: mention, but do not export "LDL" class
1324            * R/corMatrix.R: new (simple), needed for R-devel with
1325            * tests/Class+Meth.R (tstMatrixClass): 1 exception for corMatrix
1326              coerce and t() exceptions for all 5 'Mat.MatFact' classes.
1327    
1328    2006-10-19  Douglas Bates  <bates@stat.wisc.edu>
1329    
1330            * src/chm_common.h: Add R_cholmod_start to initialize cholmod to
1331            use Rprintf and R's error handling.
1332    
1333    2006-10-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1334    
1335            * R/diagMatrix.R (%*%): rep(*, each = .) in Matrix %*% diagonal.
1336            * tests/matprod.R: add tests for the bug fixed.
1337    
1338  2006-10-11  Douglas Bates  <bates@stat.wisc.edu>  2006-10-11  Douglas Bates  <bates@stat.wisc.edu>
1339    
1340          * src/HBMM.[ch]: remove HarwellBoeing format for writing.          * src/HBMM.[ch]: remove HarwellBoeing format for writing.
# Line 5  Line 1342 
1342    
1343  2006-10-06  Douglas Bates  <bates@stat.wisc.edu>  2006-10-06  Douglas Bates  <bates@stat.wisc.edu>
1344    
1345          * R/dgCMatrix.R: deprecate the writeHB function.  Use writeMM instead.          * R/d[gs]CMatrix.R: deprecate the writeHB function.  Use writeMM instead.
1346    
1347  2006-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
1348    

Legend:
Removed from v.1624  
changed lines
  Added in v.2161

root@r-forge.r-project.org
ViewVC Help
Powered by ViewVC 1.0.0  
Thanks to:
Vienna University of Economics and Business Powered By FusionForge