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revision 1716, Sat Jan 6 02:01:24 2007 UTC revision 2239, Mon Jul 28 19:26:40 2008 UTC
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1    2008-07-28  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * R/AllClass.R (diagonalMatrix): extend  "sparseMatrix" instead of
4            "denseMatrix".  This renders "scarceMatrix" dispensable and
5            invalidates part of MM's presentations on "space of Matrix
6            classes", but seems cleaner overall.
7    
8            * R/diagMatrix.R, etc: eliminate "scarceMatrix", replacing it by
9            "sparseMatrix" in method signatures;
10            further, instead of coercing to "sparseMatrix", coerce to
11            "TsparseMatrix" now.
12    
13    2008-07-26  Martin Maechler  <maechler@stat.math.ethz.ch>
14    
15            * src/dgCMatrix.c (dgCMatrix_qrsol): allow third argument 'order' in
16            .Call(.)
17            * R/sparseMatrix.R (lm.fit.sparse), src/dgCMatrix.h, src/init.c: ditto
18    
19    2008-07-24  Martin Maechler  <maechler@stat.math.ethz.ch>
20    
21            * R/dgeMatrix.R: need solve(<dge>, <sparse>) against infinite
22            recursion in new test in
23            * tests/matprod.R: testing the above and another solve() case, below
24    
25            * R/sparseMatrix.R (lm.fit.sparse): slightly more efficient for
26            e.g. triangular 'x'.
27    
28            * src/dgCMatrix.c (dgCMatrix_qrsol): use AS_CSP() hence allowing dtC*
29            * src/dgCMatrix.c (dgCMatrix_cholsol): use AS_CHM_SP() to work
30            correctly with unit-triangular x
31    
32            * src/dsCMatrix.c (dsCMatrix_Csparse_solve): use AS_CHM_SP()
33            instead of not checking diagU.
34    
35            * R/diagMatrix.R, R/Auxiliaries.R: tweaks to allow later
36            experiments where diagonalMatrix would extend sparse*.
37    
38    
39    2008-07-23  Martin Maechler  <maechler@stat.math.ethz.ch>
40    
41            * src/dgCMatrix.c (compressed_non_0_ij): for nnzero(), use
42            "x@p[ncol(x)]" instead of length(x@i).
43            * R/Auxiliaries.R (nnzero): ditto
44    
45            * src/chm_common.c (as_cholmod_sparse): Do not use LENGTH(islot)
46            since that fails for over-allocated i.
47    
48            * tests/validObj.R: more testing of over-allocated (i,x) slots
49    
50    2008-07-23  Martin Maechler  <maechler@stat.math.ethz.ch>
51    
52            * src/chm_common.c (as_cholmod_sparse): Add 4th argument
53            'sort_in_place' and set it to TRUE in call from
54            * src/Csparse.c (Csparse_validate): sort in place, making sure that
55            validObject() continues sort the columns if needed.
56    
57            * tests/validObj.R: now tests that more thoroughly, and
58            * man/CsparseMatrix-class.Rd: documents it.
59    
60    2008-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
61    
62            * src/cs_utils.c (Matrix_as_cs): add check_Udiag switch
63            * src/cs_utils.h (AS_CSP & AS_CSP__): two versions
64            * src/dtCMatrix.c (dtCMatrix_sparse_solve): no longer needs
65            diagU2N().
66    
67            * R/diagMatrix.R (.sparseDiagonal): new utility, used in "old"
68            .spDiagonal() and new .trDiagonal().
69    
70            * R/dtCMatrix.R (solve): make use of .trDiagonal()
71    
72    2008-07-19  Martin Maechler  <maechler@stat.math.ethz.ch>
73    
74            * R/Auxiliaries.R (dimNamesCheck): fix very long standing buglet,
75            stumbled upon by Michael H.
76    
77            * tests/validObj.R: testing the bug-fix
78    
79            * src/chm_common.h (AS_CHM_SP__, AS_CHM_TR__): the non-diagU2N
80            versions.
81    
82            * src/chm_common.c (as_cholmod_sparse, as_cholmod_triplet): new
83            boolean argument 'check_Udiag' (formerly implicitly was FALSE).
84    
85            * src/Csparse.c (Csparse_Csparse_prod, ...): etc: use the new
86              AS_CHM_SP() which includes diagU2N.
87    
88            * inst/include/Matrix_stubs.c (M_as_cholmod_sparse): similarly
89            adapt to 3 arguments.
90    
91    2008-07-17  Douglas Bates <bates@stat.wisc.edu>
92    
93            * [r2217] R/dtCMatrix.R, src/dtCMatrix.c, src/dtCMatrix.h, src/init.c:
94              Replace dtCMatrix_solve by more general dtCMatrix_sparse_solve and add
95              new solve method
96            * [r2216] src/cs_utils.c: Utility csp_eye in case we want to fold
97              Csparse_diagU2N functionality into Matrix_as_cs
98    
99    2008-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
100    
101            * inst/doc/factor2sparse.Rnw: revive a year-old unfinished vignette
102    
103    2008-07-16  Douglas Bates <bates@stat.wisc.edu>
104    
105            * [r2212] R/sparseMatrix.R: fac2sparse gets a drop.unused.levels
106              argument with default TRUE
107            * [r2211] inst/include/Matrix.h, inst/include/Matrix_stubs.c: Export
108              Csparse_diagU2N
109            * [r2210] R/dtCMatrix.R, man/dtCMatrix-class.Rd, src/dtCMatrix.c,
110              src/dtCMatrix.h, src/init.c: Remove vestigial methods based on the
111              parent array; new solve method for signature(a = "dtCMatrix", b =
112              "sparseMatrix")
113    
114    2008-07-14  Martin Maechler  <maechler@stat.math.ethz.ch>
115    
116            * R/diagMatrix.R (.bdiag): also keep result triangular
117    
118    2008-07-13  Douglas Bates <bates@stat.wisc.edu>
119    
120            * [r2208] src/dtCMatrix.c, src/dtTMatrix.c: Revise wording in error
121              messages
122    
123    2008-07-12  Martin Maechler  <maechler@stat.math.ethz.ch>
124    
125            * R/diagMatrix.R (.bdiag): make more sophisticated, keeping
126            symmetric- or nsparse-Matrix, also fixing the bug introduced with
127            the new version (.999375-10).
128    
129            * tests/Simple.R: regression test for the bugs.
130    
131    2008-07-07  Martin Maechler  <maechler@stat.math.ethz.ch>
132    
133            * R/sparseVector.R (spV2M): fix for "isparseVector".
134            Further, fix <diag> -> <sparseVector> coercion
135            (repSpV): add rep(<sparseVector>, .) method
136    
137            * R/sparseMatrix.R ([<-): when the RHS is a "scarce"Matrix, do *not*
138            use as.vector(.).
139    
140            * R/Tsparse.R ([<-): & [CR]sparse.R: methods for value = "sparseVector"
141    
142            * R/AllClass.R: new (hidden) class union "scarceMatrix"
143            * R/AllClass.R: sparseVector: add prototype
144    
145            * src/dsCMatrix.c (chk_nm): fix "Cholesky" check, thanks to
146            Kasper Kristensen
147    
148    2008-06-28  Martin Maechler  <maechler@stat.math.ethz.ch>
149    
150            * tests/other-pkgs.R: add more interesting Matrix -> graph
151    
152    2008-06-27  Martin Maechler  <maechler@stat.math.ethz.ch>
153    
154            * R/sparseMatrix.R (Tsp2grNEL): add 'need.uniq' argument for speed
155            improvement in "[CR]sparseMatrix" -> "graphNEL" coercion.
156    
157    2008-06-25  Martin Maechler  <maechler@stat.math.ethz.ch>
158    
159            * DESCRIPTION: release 0.999375-10 to CRAN
160    
161            * R/diagMatrix.R (.bdiag): use more efficient Bates-algorithm for
162            .bdiag().
163            * man/bdiag.Rd: update, including test.
164    
165    2008-06-24  Martin Maechler  <maechler@stat.math.ethz.ch>
166    
167            * tests/Simple.R: add minimal bdiag() checks
168    
169            * R/diagMatrix.R (bdiag): fix bdiag(diag(4:5)) case;
170              factor out the Tsparse - internal computation into new .bdiag()
171    
172    2008-06-14  Martin Maechler  <maechler@stat.math.ethz.ch>
173    
174            * R/nsparseMatrix.R: specific fast all() and any() methods.
175    
176            * src/dgTMatrix.c (MAKE_gTMatrix_to_geMatrix): better error message
177            when trying to produce too large result.
178    
179            * inst/test-tools.R (checkMatrix): add 'do.matrix' with a check for
180            very large matrices.
181    
182            * R/sparseMatrix.R (printSpMatrix2): new function, used by
183            show(<sparseMatrix>).
184    
185            * R/diagMatrix.R (show): print only diagonal entries when nrow(.) >= 50.
186    
187    2008-06-13  Martin Maechler  <maechler@stat.math.ethz.ch>
188    
189            * src/Mutils.c (m_encodeInd, m_encodeInd2):
190            * R/*.R: .Call(m_encodeInd2?, ..) instead of encodeInd2?(..).
191    
192            * R/Auxiliaries.R (encodeInd2?): care against integer overflow (for
193            big matrices): -> 2nd argument 'di' instead of 'nr' !
194    
195    2008-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
196    
197            * R/dtCMatrix.R: faster dgC* -> dtC* method
198            * tests/Simple.R: (hence removed "FIXME")
199    
200            * R/Auxiliaries.R (copyClass): add 'check = .copyClass.check'
201            which can be be turned off for possible speed gains.
202    
203    2008-06-02  Martin Maechler  <maechler@stat.math.ethz.ch>
204    
205            * R/dMatrix.R, R/Tsparse.R: get rid of some disambiguation warnings
206    
207            * R/not.R: fix !<ldiMatrix>
208            implement two old "FIXME"s:  !<ldenseMatrix> & !<ndenseMatrix>
209    
210            * R/diagMatrix.R (Ops): fix one-off thinko in
211            <diagonal> o <numeric> methods
212    
213            * inst/test-tools.R: checkMatrix(): drop0(m12) unconditionally
214    
215    2008-05-30  Martin Maechler  <maechler@stat.math.ethz.ch>
216    
217            * R/diagMatrix.R (Ops): more <diagonal> o <Matrix> methods
218            * tests/Simple.R: testing the above
219    
220    2008-05-07  Martin Maechler  <maechler@stat.math.ethz.ch>
221    
222            * NAMESPACE: also import "Ops" {found via new tools:::get_S4_generics_with_methods()}
223    
224    2008-05-03  Martin Maechler  <maechler@stat.math.ethz.ch>
225    
226            * R/Matrix.R (dimnames<-): dimnames(.) <- NULL works with a message;
227            * NAMESPACE (unname): finally exported
228    
229    2008-04-28  Martin Maechler  <maechler@stat.math.ethz.ch>
230    
231            * R/Auxiliaries.R (cholMat): possibly keep packed
232    
233            * inst/test-tools.R (checkMatrix): add fixed determinant.matrix()
234            for R < 2.7.0.
235    
236            * R/Tsparse.R ([): for triangularMatrix, check if result may be
237            triangular.
238            * tests/indexing.R: regression test
239    
240    2008-04-26  Martin Maechler  <maechler@stat.math.ethz.ch>
241    
242            * inst/test-tools.R (checkMatrix): test <Ops> not only for dMatrix
243            * R/Ops.R: more methods, for lMatrix/nMatrix
244    
245    2008-04-24  Martin Maechler  <maechler@stat.math.ethz.ch>
246    
247            * R/expm.R: new file for all expm() methods; notably new ones for
248            diagonal*, triangular*, symmetric* and also simple "matrix".
249    
250    2008-04-23  Martin Maechler  <maechler@stat.math.ethz.ch>
251    
252            * R/dsyMatrix.R: setAs(.) rather than setIs(.)  "to dpoMatrix"
253    
254            * inst/test-tools.R (assert.EQ.mat): better message when not equal
255    
256            * src/dgeMatrix.c (dgeMatrix_matrix_crossprod): allow integer RHS.
257    
258            * R/AllClass.R (ddiMatrix,ldiMatrix): extend [dl]Matrix instead of
259            [dl]denseMatrix {identical slots; but more logical method dispatch}
260    
261    2008-04-23  Martin Maechler  <maechler@stat.math.ethz.ch>
262    
263            * R/sparseMatrix.R (summary): use length(<i-slot>) instead of nnzero()
264    
265            * R/diagMatrix.R (determinant): method
266    
267    2008-04-22  Martin Maechler  <maechler@stat.math.ethz.ch>
268    
269            * src/dsCMatrix.c (dsCMatrix_Cholesky): suppress CHOLMOD printing too
270    
271            * R/Rsparse.R (.viaC.to.R): uplo fix for symmetric & triangular
272    
273            * R/dsCMatrix.R (determinant): switch to use Cholesky( 'LDL' ) and
274            its diagonal
275    
276    2008-04-21  Martin Maechler  <maechler@stat.math.ethz.ch>
277    
278            * R/dMatrix.R (Summary): short-cut for prod(<sparse>)
279    
280            * R/not.R: fix !<"U"-diag-ltrMatrix> ; drop {R < 2.6.0}-branch
281    
282            * R/Auxiliaries.R (tT2gT): fix for "U"-diag-ltTMatrix
283    
284            * R/AllClass.R: ltTMatrix validity: call (more stringent) tTMatrix_validate
285    
286    2008-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
287    
288            * R/Ops.R (Ops.x.x): aux.function, not just for (dMatrix,dMatrix)
289    
290            * R/Ops.R (.do.Logic.lsparse): fix NA case
291    
292            * R/Tsparse.R (replTmat): fix r.sym case, using indTri()
293    
294            * R/Auxiliaries.R (nnzero): fix special cases, using
295            * R/Auxiliaries.R (indDiag): new utility
296            * R/Auxiliaries.R (indTri): new argument 'diag'
297    
298            * R/dMatrix.R: Summmary(<ddenseMatrix>): different branch for dsy*
299    
300    2008-04-18  Martin Maechler  <maechler@stat.math.ethz.ch>
301    
302            * R/diagMatrix.R: "Summary" methods, and more "Arith" / "Ops"
303    
304            * src/Csparse.c (Csparse_drop): preserve (uplo,diag) for
305            ".tCMatrix" triangular matrix.
306    
307            * R/Auxiliaries.R (drop0): use diagU2N(); according to helpfile,
308            'clx' can be class *or* class representation.
309            (nnzSparse): new.
310            (non0ind): new 'xtendSymm' argument; used in
311            * R/Ops.R:
312    
313            * R/pMatrix.R: more efficient determinant() method
314    
315    2008-04-17  Martin Maechler  <maechler@stat.math.ethz.ch>
316    
317            * [disactivated] R/Matrix.R (det): det() as base::det(), but with Matrix environment
318            * [disactivated] NAMESPACE: export(det)
319    
320            * R/diagMatrix.R (mkDiag): new substitute for diag()
321    
322            * R/Auxiliaries.R (nnzero): fix for "diagU2N"-case
323            (as0, as1): new utility.
324    
325            * R/Csparse.R (diag, band): need diagU2N()
326    
327            * src/dgeMatrix.c (get_norm): return NA when 'x' slot has NA/NaN.
328    
329            * R/lMatrix.R: coerce(nMatrix |-> lMatrix) fix
330    
331            * R/Ops.R (Compare): fix <nsp> o <nsp> case
332    
333            * R/nsparseMatrix.R, R/pMatrix.R: is.na() method
334    
335    2008-04-16  Martin Maechler  <maechler@stat.math.ethz.ch>
336    
337            * R/Auxiliaries.R (signPerm): new utility for
338            * R/Auxiliaries.R (detSparseLU): determinant() via sparseLU
339    
340            * src/dsCMatrix.c (dsCMatrix_LDL_D): suppress 'CHOLMOD warning';
341            since we have our own error handler (and can use tryCatch() from R).
342    
343    2008-04-15  Martin Maechler  <maechler@stat.math.ethz.ch>
344    
345            * R/dgTMatrix.R (image): ha! set col=NA if lwd is small -- very nice!
346    
347            * R/dsCMatrix.R (determinant): use tryCatch() and switch to lu()
348            when not positive definite.
349    
350            * R/Auxiliaries.R (asTri): new auxiliary
351            (non0.i): make *much* faster for Tsparse with many non-zero
352            entries; add 'uniqT = TRUE' argument to be used when sorting is undesired.
353    
354            * tests/Class+Meth.R (dotestMat): now build on checkMatrix() from
355            test-tools.R , see below
356    
357            * R/dMatrix.R: fix "Summary" method: + diagU2N()
358    
359            * NAMESPACE, R/Matrix.R: add mean() method
360    
361    2008-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
362    
363            * R/dgTMatrix.R (image): allow to *not* take abs(), and use
364            cold-hot colors; try *changed* default useAbs = FALSE
365            * man/image-methods.Rd:  nice examples
366    
367    2008-04-11  Martin Maechler  <maechler@stat.math.ethz.ch>
368    
369            * inst/test-tools.R (checkMatrix): new function for modularizing part
370            of tstMatrixClass() in tests/Class+Meth.R
371    
372            * R/dsCMatrix.R: coercion from "matrix"
373            * R/ltTMatrix.R, R/ntTMatrix.R: ditto (change it).
374    
375            * tests/Class+Meth.R (tstMatrixClass): some cleanup;
376            add test for as(matrix(,0,0), <class>)
377    
378    2008-04-09  Martin Maechler  <maechler@stat.math.ethz.ch>
379    
380            * src/dgeMatrix.c (dgeMatrix_determinant): for n == 0,
381            work as determinant(matrix(,0,0)).
382    
383            * src/dgCMatrix.c (dgCMatrix_LU): return {L,U} as dtCMatrix
384            * man/sparseLU-class.Rd: ditto
385    
386            * R/dgCMatrix.R (determinant): method building on lu()
387            * R/sparseMatrix.R, Matrix.R, ...: ditto
388    
389            * R/Auxiliaries.R (mkDet): auxiliary for determinant()
390    
391    2008-04-07  Martin Maechler  <maechler@stat.math.ethz.ch>
392    
393            * R/sparseMatrix.R (summary<sparseMatrix>): no 'x' column for
394            pattern matrices.
395    
396    2008-04-02  Martin Maechler  <maechler@stat.math.ethz.ch>
397    
398            * src/dense.c (dense_to_Csparse): all declarations *before*
399            R_CheckStack(); needed e.g. for ancient gcc 2.96.
400    
401    
402    2008-03-29  Martin Maechler  <maechler@stat.math.ethz.ch>
403    
404            * DESCRIPTION (Version): 0.999375-9 --- need to release
405            for R-devel (and R 2.7.0 alpha soon).
406    
407            * R/AllClass.R: drop "double" from "atomicVector" class union
408    
409            * R/AllGeneric.R (rcond): check for base::rcond instead of R version
410            * R/dgeMatrix.R: ditto
411    
412            * R/sparseMatrix.R (summary): count NAs
413    
414            * inst/doc/Intro2Matrix.Rnw: changes, aim for *one* introduction.
415    
416    2008-03-28  Martin Maechler  <maechler@stat.math.ethz.ch>
417    
418            * R/AllGeneric.R: rcond(., norm) instead of rcond(., type), in
419            order to become compatible to new R 2.7.0 base::rcond().
420    
421    2008-03-25  Martin Maechler  <maechler@stat.math.ethz.ch>
422    
423            * DESCRIPTION (Version,Date): 0.999375-8 --- released to CRAN
424    
425            * R/diagMatrix.R (Ops): fix newly introduce bug in <.di> o <numeric>
426    
427            * inst/test-tools.R (isValid): new utility, used much in
428            * tests/simple.R:
429    
430            * man/BunchKaufman-methods.Rd: added too
431    
432    2008-03-24  Martin Maechler  <maechler@stat.math.ethz.ch>
433    
434            * R/dsyMatrix.R: add BunchKaufman() methods.
435            * R/dspMatrix.R:
436    
437            * src/init.c: add dsyMatrix_trf
438    
439    2008-03-23  Douglas Bates <bates@stat.wisc.edu>
440    
441            * DESCRIPTION (Version): release 0.999375-7
442            * src/CHMfactor.c (CHMfactor_update): fix
443    
444    2008-03-22  Martin Maechler  <maechler@stat.math.ethz.ch>
445    
446            * src/dsCMatrix.c (dsCMatrix_LDL_D): cleanup, also using
447            internal_chm_factor().
448    
449            * R/AllGeneric.R: do *not* define a "chol" generic
450                    (but rather use the implicit one *without* making pivot
451                    part of the signature)
452            * R/*.R: drop the 'pivot' from chol's signature and make
453                    'pivot=FALSE' a default argument of method definitions.
454    
455            * .Rbuildignore: add 'wrld_1deg': I.e. do not put it into released
456            version of Matrix
457    
458    2008-03-18  Martin Maechler  <maechler@stat.math.ethz.ch>
459    
460            * R/Tsparse.R (.T.2.n): drop 0's before coercion to "nMatrix"
461    
462            * R/sparseMatrix.R (is.na): new simple method
463            * R/denseMatrix.R (is.na): ditto.
464    
465            * R/diagMatrix.R (.symDiagonal): newly exported utility.
466    
467            * R/diagMatrix.R (Ops): <diag> * <numeric> should not become dgeMatrix!
468    
469            * src/UFsparse_download.sh: -->
470            * src/CHOLMOD/: update to CHOLMOD version 1.6 (Nov.2007)
471    
472    2008-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
473    
474            * src/dsCMatrix.c (dsCMatrix_LDL_D): even faster utility with same
475            functionality; barely tested in
476            * tests/factorizing.R
477    
478            * src/Csparse.c (diag_tC): new functionality to enable faster
479            determinant(<dsCMatrix>, .) in
480            * R/dsCMatrix.R
481    
482    2008-03-17 18:53  Douglas Bates <bates@stat.wisc.edu>
483    
484            * R/CHMfactor.R, inst/include/Matrix.h, inst/include/Matrix_stubs.c,
485              src/CHMfactor.c, src/CHMfactor.h,
486              man/CHMfactor-class.Rd, src/init.c, tests/factorizing.R:
487              Log-determinant of the parent matrix from a CHMfactor object as
488              chm_factor_ldetL2; documentation and support
489    
490    2008-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
491    
492            * R/dsCMatrix.R: enable determinant(<dsCMatrix>, .) via chol(.)
493    
494    2008-03-14  Martin Maechler  <maechler@stat.math.ethz.ch>
495    
496            * R/dsCMatrix.R: setAs(., "dsCMatrix") but with a deprecation
497            warning.
498    
499    2008-03-13  Martin Maechler  <maechler@stat.math.ethz.ch>
500    
501            * DESCRIPTION (Version, Date): bug-fix release 0.999375-6
502    
503            * R/diagMatrix.R (diag2tT.u): utility to be smarter in
504              <diagonal> o <sparse_triangular>
505              setAs(., "nMatrix") added.
506    
507            * R/diagMatrix.R (Diagonal): Diagonal(4, x=3) now works too
508    
509            * R/Auxiliaries.R (.diagU2N): more careful coercion in 2 steps
510                    new argument 'checkDense = FALSE'.
511    
512    
513    2008-03-07  Martin Maechler  <maechler@stat.math.ethz.ch>
514    
515            * src/dgeMatrix.c (dgeMatrix_exp): fix the octave-origin bug in the
516            back-permutation of the matrix exponential.
517    
518            * tests/matr-exp.R: test the fix (for an example where expm() was wrong).
519    
520            * DESCRIPTION (Date,Version): ready to release 0.999375-5
521    
522            * tests/simple.R: testing diagN2U
523    
524    2008-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
525    
526            * R/Auxiliaries.R (diagN2U): interface to
527    
528            * src/Csparse.c (Csparse_diagN2U): .Call()able SEXP version of chm_diagN2U()
529    
530            * tests/matprod.R: test for triangularity preserving <dtC> %*% <dtC>
531    
532    2008-03-05  Martin Maechler  <maechler@stat.math.ethz.ch>
533    
534            * src/chm_common.c (chm_diagN2U): new utility.
535    
536            * src/Csparse.c (Csparse_Csparse_crossprod, Csparse_Csparse_prod):
537            make use of chm_diagN2U() and hence now preserve triangularity and
538            unit-triangularity.
539    
540            * DESCRIPTION (LicenseDetails): new; such that 'License:' becomes "canonical"
541    
542    2008-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
543    
544            * R/diagMatrix.R (subDiag): fix when x[..] became a vector
545    
546            * src/Tsparse.c (Tsparse_diagU2N): new utility, necessary for e.g.
547            * src/Csparse.c (Csparse_crossprod): use [CT]sparse_diagU2N() !!
548    
549            * R/Auxiliaries.R (.diagU2N): make use of new Tsparse_diagU2N
550    
551            * R/Ops.R ("-" (<sparseMatrix>)): use diagU2N()
552    
553            * src/chm_common.c (AS_CHM_FINISH): add note about problem
554            for triangular (diag = "U").
555    
556    2008-02-21  Martin Maechler  <maechler@stat.math.ethz.ch>
557    
558            * R/Auxiliaries.R (as_Csparse2): drop this, replacing by
559            * R/bind.R:  .Call(dense_to_Csparse, *)
560    
561    2008-02-20  Martin Maechler  <maechler@stat.math.ethz.ch>
562    
563            * R/Matrix.R (Matrix): no longer use coercions to specific classes
564                    (since we are discouraging them in user code).
565    
566            * tests/*.R: also replaces coercions to specific classes by
567            coercions to super classes.
568    
569            * R/denseMatrix.R (.dense2C): simplified by using forceSymmetric()
570    
571    
572    2008-02-19  Martin Maechler  <maechler@stat.math.ethz.ch>
573    
574            * man/CAex.Rd: example: coerce to symmetric*, not dsC*
575    
576            * src/dense.c (dense_band): generalized from ddense_band
577    
578            * R/ddenseMatrix.R (.trilDense,.triuDense, .bandDense):
579              now for "denseMatrix" (instead of just "ddense*"); much
580              simplified setMethod()s for these.
581    
582            * src/dense.c (dense_to_symmetric): generalized from ddense_*
583    
584    2008-02-18  Martin Maechler  <maechler@stat.math.ethz.ch>
585    
586            * R/AllGeneric.R: forceSymmetric() generic: fast no-checking
587            version of as(*, "symmetricMatric").
588    
589            * src/dense.c (ddense_to_symmetric): add 'symm_test' argument, and
590            * R/symmetricMatrix.R: set it TRUE in coercion to "symmetricMatrix"
591    
592    2008-02-16  Martin Maechler  <maechler@stat.math.ethz.ch>
593    
594            * R/Matrix.R (subset.ij): utility, as first step to faster
595               M [ <ij-matrix> ] indexing.
596    
597            * R/Matrix.R (.M.sub.i.logical): M[ <logical> ] : try better.
598    
599            * src/dense.c (ddense_symmpart, ddense_skewpart): new functions
600            for more efficient symmpart() and skewpart() methods.
601    
602            * src/Mutils.c (equal_string_vectors): utility
603    
604            * src/dense.c (ddense_to_symmetric): new function used in
605    
606            * R/symmetricMatrix.R: setAs(., "symmetricMatrix")
607    
608            * R/sparseMatrix.R, et_al (isSymmetric): add '...' to formals, in
609            order to match the generic (and evade .local(..)).
610    
611            * R/dsCMatrix.R: dgC -> dsC: use C code!
612    
613            * NAMESPACE, R/AllGeneric.R (symmpart, skewpart): new functions
614            as per TODO
615    
616            * R/Auxiliaries.R (setZero, all0Matrix): new utilities
617    
618            * R/symmetricMatrix.R: obvious symmpart(), skewpart() methods
619    
620    
621    2008-02-15  Martin Maechler  <maechler@stat.math.ethz.ch>
622    
623            * R/Ops.R (.Arith.Csparse): use diagU2N when needed in triangular
624    
625            * R/Auxiliaries.R (non0.i): take out of non0ind
626    
627            * R/ddenseMatrix.R (.trilDense, .triuDense, .bandDense):
628            make tril(), triu(), band() work for "matrix" and all "dense*"
629    
630            * R/triangularMatrix.R (.tri[lu].tr): need .diagU2N(*)
631            * tests/simple.R: test the fix above
632    
633            * R/sparseMatrix.R ([): simplification: no coerce to <general>
634                    before we use as(., <Tsparse>)[...] anyway
635    
636            * R/Rsparse.R (.viaC.to.R): mostly instead of .viaC.to.dgR()
637    
638            * R/triangularMatrix.R (isTriangular): methods for all subclasses
639            instead of "triangularMatrix" -- just to disambiguate
640    
641    2008-02-14  Martin Maechler  <maechler@stat.math.ethz.ch>
642    
643            * tests/Class+Meth.R (dotestMat): add m[FALSE, FALSE] { <-> TODO}
644            * tests/indexing.R: example that fails above
645    
646    2008-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
647    
648            * R/Matrix.R (.M.sub.i.2col): fix for logical matrix indexing
649            * R/Tsparse.R (.TM.sub.i.2col, .TM.repl.i.2col): ditto;
650                    now, M[lower.tri(M)] and  M[lower.tri(M)] <- v  work better
651    
652            * src/Tsparse.c (Tsparse_to_tCsparse): new fast utility.
653            * src/Tsparse.h, init.c: ditto
654            * R/Auxiliaries.R (isTriT): new; faster than going via Csparse
655                 both isTriC() and isTriT() now return TRUE with "kind" or FALSE.
656            * R/sparseMatrix.R (isTriangular): hence simplified
657    
658    2008-01-24  Martin Maechler  <maechler@stat.math.ethz.ch>
659    
660            * R/Ops.R (.Arith.Csparse): new utility factored out of former
661              <dgC> o <dgC>, extended for triangular and also used in  <dtC> o <dtC>.
662    
663    2008-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
664    
665            * tests/factorizing.R (checkSchur): and more tests for checking Schur()
666    
667            * inst/test-tools.R (isOrthogonal): new function; also file restructured
668    
669    2008-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
670    
671            * R/ngTMatrix.R: allow as(<numeric matrix>, "ngTMatrix") and hence
672            coercion to "nMatrix" and "pMatrix"
673    
674            * R/AllClass.R: "Schur" class;  "number" class union
675            * man/number-class.Rd:
676            * man/Schur-class.Rd:
677    
678            * R/eigen.R (.dgeSchur): utility, and return "Schur" class
679            (.simpleSchur): Schur() method for diagonal matrices
680            (.triSchur):    Schur() method for triangular matrices
681            (Schur.sym):    Schur() for symmetric matrices {building on eigen()}.
682    
683    
684    2008-01-21  Martin Maechler  <maechler@stat.math.ethz.ch>
685    
686            * src/dgCMatrix.c (dgCMatrix_QR): set @Dim slot (as per doc)
687    
688    2008-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
689    
690            * R/CHMfactor.R (solve): method for b="numeric", but also b="ANY"
691                    in order to ensure 'system = *' is not lost;
692                    formals()$system instead of cut&paste.
693            * tests/factorizing.R: test solve(<CHM..>, <numeric>)
694    
695    2008-01-11  Martin Maechler  <maechler@stat.math.ethz.ch>
696    
697            * DESCRIPTION (Date): make ready for release --> 0.999375-4
698    
699            * R/dgeMatrix.R: fix rcond() method for "dgeMatrix".
700    
701    2007-12-08  Martin Maechler  <maechler@stat.math.ethz.ch>
702    
703            * R/pMatrix.R: as(*, "matrix") now returns 0/1 *integer* matrix,
704                    and hence does as.vector(.).
705            * man/pMatrix-class.Rd: docs
706            * R/sparseMatrix.R: fix for printing "integer sparse"
707    
708            * tests/Class+Meth.R (tstMatrixClass): test M[FALSE], M[2] etc
709    
710            * R/Matrix.R and others: use "exact" function argument list for
711                    both "["   : (x, i,j, ..., drop)
712                    and  "[<-" : (x, i,j, ..., value)
713    
714            * R/denseMatrix.R: M[i] and M[i] <- v  (i vector) now work
715            * R/Tsparse.R (replTmat):    ditto
716            * R/diagMatrix.R (replDiag): ditto
717            * R/Csparse.R (replCmat):    ditto {was it worth the pain?}
718            * tests/indexing.R: testing the above
719    
720    2007-12-07  Martin Maechler  <maechler@stat.math.ethz.ch>
721    
722            * R/sparseMatrix.R (cov2cor): method for sparse matrices
723    
724            * R/diagMatrix.R ([<-): fix   D[ cbind(i,j) ] <- v
725    
726            * R/bind2.R: fix for Rsparse* and rbind2(dense,dense)
727    
728            * tests/Class+Meth.R: test cbind2, rbind2  and  diag<-
729    
730    2007-12-06  Martin Maechler  <maechler@stat.math.ethz.ch>
731    
732            * R/Matrix.R: "generic" cov2cor() method
733    
734            * R/nearPD.R: new 'only.values', 'keepDiag' arguments;
735                    speed up Q %*% D %*% t(Q)
736            * tests/dpoMatrix.R: test nearPD()
737    
738    2007-12-05  Doug Bates and Martin Maechler
739    
740            * R/sparseMatrix.R: xtabs(*, sparse=.) function; an extention of
741            stats::xtabs() allowing to create sparse matrices.
742    
743    2007-10-08  Martin Maechler  <maechler@stat.math.ethz.ch>
744    
745            * DESCRIPTION (Version): *-4 (released *-3 two days ago)
746    
747    2007-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
748    
749            * R/pMatrix.R: solve(<Matrix>, <pMatrix>)
750    
751    2007-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
752    
753            * R/LU.R: solve() method for "denseLU"
754    
755    2007-10-01  Martin Maechler  <maechler@stat.math.ethz.ch>
756    
757            * DESCRIPTION (Version): 0.999375-3 preparing for release
758    
759            * R/AllGeneric.R: simplify  if(.) .. else .. for R <= 2.5.1
760    
761            * R/Matrix.R (Matrix): .Internal(matrix(..)) different for R >= 2.7.0
762    
763    2007-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
764    
765            * R/pMatrix.R (.m.mult.pMat): fix <matrix> %*% <pMatrix>,
766              thanks to Kasper Kristensen.
767            * tests/matprod.R: regression test for that.
768    
769    2007-09-23 17:32  Douglas Bates <bates@stat.wisc.edu>
770    
771            * [r4778] R/AllGeneric.R: Check R version before defining generics for
772              primitives
773    
774    2007-09-13  Martin Maechler  <maechler@stat.math.ethz.ch>
775    
776            * R/denseMatrix.R (rcond): method
777            * R/sparseQR.R (rcond): method, use x or t(x)
778    
779    2007-09-12  Martin Maechler  <maechler@stat.math.ethz.ch>
780    
781            * R/dgeMatrix.R (rcond): method: work via qr.R() for non-square
782            matrices.
783            * R/sparseMatrix.R: Ditto for all other rcond() method definitions.
784    
785            * man/rcond.Rd: mention the more general definition, and add
786            example for non-square matrices.
787    
788            * man/chol.Rd: new file, for the S4 chol() generic and all methods.
789    
790    2007-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
791    
792            * R/sparseQR.R: add qr.R() method [to be used for rcond()]
793    
794    2007-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
795    
796            * R/Matrix.R ([<-): add (Matrix,missing,ANY,Matrix) etc
797            * tests/indexing.R: add new regression for the above cases.
798    
799    2007-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
800    
801            * src/Mutils.h (__sun): clause for alloca.h on Solaris
802    
803    2007-08-16  Martin Maechler  <maechler@stat.math.ethz.ch>
804    
805            * DESCRIPTION (Date, Version): 0.999375-2
806    
807    2007-08-15  Martin Maechler  <maechler@stat.math.ethz.ch>
808    
809            * R/HBMM.R (readMM): make work for pattern matrices as well
810    
811    2007-08-14 13:07  Douglas Bates <bates@stat.wisc.edu>
812    
813            * [r4730] src/Mutils.h: declare alloca
814            * [r4734] NAMESPACE, R/AllGeneric.R, R/Csparse.R, R/HBMM.R, R/Tsparse.R,
815              R/dgCMatrix.R, R/dgTMatrix.R, R/dsCMatrix.R, R/dsTMatrix.R,
816              man/externalFormats.Rd, src/Csparse.c, src/Csparse.h, src/DEPS.mkf,
817              src/HBMM.c, src/HBMM.h, src/Mutils.h, src/SOURCES_C.mkf, src/init.c,
818              src/mmio.c, src/mmio.h: Remove deprecated function writeHB and its
819              methods; switch writeMM to use CHOLMOD code; repair readMM
820    
821    2007-08-14  Martin Maechler  <maechler@stat.math.ethz.ch>
822    
823            * R/nearPD.R, man/nearPD.Rd (nearPD): new function built on Jens
824            Oehlschlaegel's ... result type still to be discussed!
825    
826    2007-08-10  Martin Maechler  <maechler@stat.math.ethz.ch>
827    
828            * man/image-methods.Rd: new, combining all image() methods
829    
830    2007-08-09  Martin Maechler  <maechler@stat.math.ethz.ch>
831    
832            * R/dgCMatrix.R: define qr() and lu() methods for "sparseMatrix"
833            to work via dgC...
834    
835            * R/Matrix.R (Matrix): special treatment for "table" (S3)
836    
837    2007-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
838    
839            * R/dgTMatrix.R (image): change defaults to
840                    aspect = "iso", colorkey = FALSE
841    
842    2007-08-06  Martin Maechler  <maechler@stat.math.ethz.ch>
843    
844            * src/dsyMatrix.c (dsyMatrix_matrix_mm): 'b' might be matrix;
845            must copy its *expanded* x slot before LAPACK call.
846    
847            * tests/matprod.R: test the last days' changes.
848    
849    2007-08-06 16:43  Douglas Bates <bates@stat.wisc.edu>
850    
851            * [r4712] inst/include/Matrix_stubs.c: Change R_cholmod_printf in stubs
852              as well as in sources
853            * [r4713] src/dsyMatrix.c: Duplicate the contents of the RHS before
854              Lapack call
855    
856    2007-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
857    
858            * R/Matrix.R (%*%, crossprod, tcrossprod): add method for
859                    ("Matrix", "matrix") which is needed in some cases.
860            Ditto for solve().
861    
862            * R/colSums.R (.as.dge.Fun): need ddenseMatrix methods to avoid
863            infinite recursion in dispatch for some cases.
864    
865    2007-08-02 08:48  Martin Maechler <maechler@stat.math.ethz.ch>
866    
867            * [r4693] src/chm_common.c: R_cholmod_printf() instead of Rprintf() just
868              so pointers match
869    
870    2007-08-02  Martin Maechler  <maechler@stat.math.ethz.ch>
871    
872            * DESCRIPTION (Date): set ready for release -- 0.999375-1
873    
874    2007-08-01 15:44  Douglas Bates <bates@stat.wisc.edu>
875    
876            * [r4686] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
877              src/chm_common.c, src/chm_common.h: Change API for
878              numeric_as_chm_dense and N_AS_CHM_DN
879    
880    2007-08-01  Martin Maechler  <maechler@stat.math.ethz.ch>
881    
882            * src/dtrMatrix.c (dtrMatrix_matrix_mm): fix dimensionality check (!)
883            * tests/matprod.R: regr.test for it
884    
885    2007-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
886    
887            * R/dMatrix.R: fix from Brian for   Math2(., digits = "missing")
888            * tests/group-methods.R: and regression-test it
889    
890    2007-07-19 19:45  Douglas Bates <bates@stat.wisc.edu>
891    
892            * [r4642] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
893              inst/include/cholmod.h, src/chm_common.c, src/init.c: Export
894              triplet_to_sparse, documentation, use typedefs
895    
896    2007-07-18  Martin Maechler  <maechler@stat.math.ethz.ch>
897    
898            * man/dpoMatrix-class.Rd: added 'corMatrix' example
899    
900            * src/dsyMatrix.[ch] (dsyMatrix_as_matrix): new 'keep_dimnames' arg
901            * src/dtrMatrix.[ch] (dtrMatrix_as_matrix): ditto
902            * src/init.c, R/dsyMatrix.R, R/dtrMatrix.R, R/lgTMatrix.R: ditto
903    
904            * R/lsparseMatrix.R: bug fix in "all" method
905            * R/Ops.R (.do.Logic.lsparse): "|" bug in borderline case
906    
907            * R/dsyMatrix.R (coerce->dsTMatrix): (i,j) slots should *not* have names
908            * R/ngTMatrix.R (coerce->ngTMatrix): ditto;
909                    + matrix |-> nMatrix coercion
910            * R/pMatrix.R: + setAs()  to dMatrix and from nMatrix
911            * man/pMatrix-class.Rd: ditto
912    
913            * R/Matrix.R (Summary): method for non-dMatrix
914    
915            * tests/Class+Meth.R (extraValid): new check about "dirty" slots
916            * tests/Class+Meth.R (tstMatrixClass): test norm(.);
917                    test all Summary methods.
918    
919    2007-07-16  Martin Maechler  <maechler@stat.math.ethz.ch>
920    
921            * R/dgeMatrix.R (norm, rcond): methods for 'matrix'
922    
923    2007-07-14  Martin Maechler  <maechler@stat.math.ethz.ch>
924    
925            * R/sparseMatrix.R (norm): simple methods for sparseMatrix
926    
927            * R/pMatrix.R (t?crossprod): methods for pMatrix
928    
929    2007-07-10  Douglas Bates  <bates@stat.wisc.edu>
930    
931            * src/dgeMatrix.c (dgeMatrix_colsums): Get the logic straight.
932    
933    2007-07-09 20:45  Douglas Bates <bates@stat.wisc.edu>
934    
935            * [r4579] src/dgeMatrix.c: Untangle horrible code in dgeMatrix_colsums
936              trying to fix a subtle bug - which has been somewhere else.
937    
938    2007-07-09 19:43  Martin Maechler <maechler@stat.math.ethz.ch>
939    
940            * [r4578] src/dgeMatrix.c: "cleaned" dgeMatrix_colsums() - but did not
941              solve the bug
942    
943    2007-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
944    
945            * src/dgCMatrix.c (compressed_to_TMatrix):
946    
947    2007-07-07  Martin Maechler  <maechler@stat.math.ethz.ch>
948    
949            * src/Csparse.c (Rsparse_validate): new, to have some validity
950            checking for RsparseMatrix
951            * src/dgCMatrix.c (xRMatrix_validate): ditto
952            * src/dtCMatrix.c (tRMatrix_validate): ditto
953    
954    2007-07-07  Douglas Bates <bates@stat.wisc.edu>
955    
956            * [r4567] R/AllClass.R: Slots already in RsparseMatrix were redefined in
957              lgRMatrix
958            * [r4568] DESCRIPTION: Prepare for bug-fix release
959            * [r4570] src/CHOLMOD/Check/cholmod_write.c: Include cholmod_matrixops.h
960              for declaration of cholmod_symmetry
961    
962    2007-07-06  Martin Maechler  <maechler@stat.math.ethz.ch>
963    
964            * DESCRIPTION (Version): 0.999375 merged into the trunk; ready for
965            release.
966    
967    2007-07-06 14:11  Douglas Bates <bates@stat.wisc.edu>
968    
969            * [r4559] src/iohb.c, src/iohb.h: Remove Harwell-Boeing input/output
970              functions - no longer used
971            * [r4560] src/HBMM.c, src/Mutils.c, src/dgTMatrix.c, src/dgeMatrix.c,
972              src/dspMatrix.c, src/dsyMatrix.c, src/dtCMatrix.c,
973              src/factorizations.c, src/sparseQR.c: Replace most calls to Calloc by
974              Alloca
975    
976    2007-07-06 13:14  Martin Maechler <maechler@stat.math.ethz.ch>
977    
978            * [r4558] inst/doc/Comparisons.Rnw, src/CHMfactor.c, src/Csparse.c,
979              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dense.c,
980              src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c, src/sparseQR.c,
981              src/t_gCMatrix_colSums.c: more R_CheckStack()s
982    
983    2007-07-05 18:12  Douglas Bates <bates@stat.wisc.edu>
984    
985            * [r4550] inst/include/Matrix.h: Add the macro N_AS_CHM_DN to "alloca"
986              the required amount of memory then call M_numeric_as_chm_dense.
987            * [r4556] src/Mutils.h, src/dgCMatrix.c: Define and use the Alloca macro
988              (like Calloc but calling alloca)
989    
990    2007-07-05  Martin Maechler  <maechler@stat.math.ethz.ch>
991    
992            * R/sparseMatrix.R (printSpMatrix): renamed from prSpMatrix()
993            and extended with more sophisticated 'col.names' option.
994            * NAMESPACE: export  printSparseMatrix()
995            * man/printSpMatrix.Rd: document, incl. examples
996    
997    2007-07-04 16:21  Douglas Bates <bates@stat.wisc.edu>
998    
999            * [r4543] src/cs_utils.c, src/cs_utils.h, src/dgCMatrix.c,
1000              src/dtCMatrix.c, src/sparseQR.c: CSP typedef for *cs and macro
1001              AS_CSP. API change - pass the empty structure to Matrix_as_cs.
1002    
1003    2007-07-04  Martin Maechler  <maechler@stat.math.ethz.ch>
1004    
1005            * DESCRIPTION (Version): 0.99875-4
1006    
1007            * tests/Class+Meth.R (tstMatrixClass): add dimnames, and hence test
1008            some dimnames perservation.
1009    
1010            * R/dsTMatrix.R (t-method): keep dimnames
1011            * R/dtTMatrix.R:  ditto
1012    
1013            * R/sparseMatrix.R (prSpMatrix): print colnames when non-trivial
1014            and ncol(.) < 10
1015    
1016            * src/cs_utils.c: drop check_class() and use Matrix_check_class()
1017            from Mutils.h
1018    
1019            * src/lgCMatrix.c ([ln]csc_to_matrix): no longer lose dimnames,
1020            e.g. in as(<ngCMatrix>, "matrix")
1021    
1022    2007-07-01 13:27  Douglas Bates <bates@stat.wisc.edu>
1023    
1024            * [r4529] .: Create a branch for the API changes from the 0.99875
1025              series to the 0.999375 series
1026            * [r4530] DESCRIPTION, inst/include/Matrix.h,
1027              inst/include/Matrix_stubs.c, src/CHMfactor.c, src/Csparse.c,
1028              src/Mutils.h, src/Tsparse.c, src/chm_common.c, src/chm_common.h,
1029              src/dense.c, src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c,
1030              src/t_gCMatrix_colSums.c: API change - pass the empty structure to the
1031              as_cholmod_x functions
1032    
1033    2007-06-30 09:05  Martin Maechler <maechler@stat.math.ethz.ch>
1034    
1035            * [r4527] trunk/Matrix/DESCRIPTION, trunk/Matrix/NAMESPACE,
1036              trunk/Matrix/inst/doc/Comparisons.Rnw: add session- and hardware-info
1037              to Comparisons
1038    
1039    >>>>>>> .merge-right.r4561
1040    2007-06-29  Martin Maechler  <maechler@stat.math.ethz.ch>
1041    
1042            * DESCRIPTION (Version): 0.99875-3 ready to be released.
1043    
1044            * R/sparseMatrix.R (spMatrix): make spMatrix(3,4) working
1045    
1046            * R/AllGeneric.R: set "Math" (and "Math2") group generics in a way
1047            that should also work in a future version of R.
1048    
1049    2007-06-21  Martin Maechler  <maechler@stat.math.ethz.ch>
1050    
1051            * NAMESPACE, R/AllClass.R: "xsparseVector" class union.
1052    
1053            * R/sparseVector.R: more *sparseVector coercions, notably for
1054            non - double ones.
1055    
1056    2007-06-19  Martin Maechler  <maechler@stat.math.ethz.ch>
1057    
1058            * R/colSums.R: new file for all (col|row)(Sums|Means) methods,
1059              notably the new ones building on the new .Call(.)s:
1060    
1061            * src/dgCMatrix.c (DEF_gCMatrix_COLSUMS): use to define
1062            all 4 of [dlin]gCMatrix_colSums().
1063    
1064    2007-06-18 16:12  Douglas Bates <bates@stat.wisc.edu>
1065    
1066            * [r4472] src/Syms.h, src/init.c: Added Matrix_lengthSym
1067            * [r4473] src/dgCMatrix.c: Modified dgCMatrix_colSums for sparseVector
1068              result
1069    
1070    2007-06-16  Martin Maechler  <maechler@stat.math.ethz.ch>
1071    
1072            * R/kronecker.R: fix typo (could lead to inf.recursion)
1073            * test/simple.R: testing that
1074    
1075            * R/sparseMatrix.R (prSpMatrix): change to be used as print()
1076            method as well (which can have arguments, show() can't).
1077    
1078    2007-06-16 15:52  Douglas Bates <bates@stat.wisc.edu>
1079    
1080            * [r4466] R/dgCMatrix.R, src/dgCMatrix.c, src/dgCMatrix.h, src/init.c:
1081              added dgCMatrix_colSums for [col,row][Sums,Means]
1082    
1083    2007-06-15 23:15  Douglas Bates <bates@stat.wisc.edu>
1084    
1085            * [r4460] R/sparseMatrix.R, man/dgCMatrix-class.Rd, src/dgCMatrix.c,
1086              src/dgCMatrix.h, src/init.c: added lm.fit.sparse (unexported),
1087              coercion of "factor" to "dgCMatrix" and dgCMatrix_cholsol
1088            * [r4461] R/AllClass.R, man/sparseMatrix-class.Rd: draft "indicators"
1089              class
1090            * [r4463] R/sparseMatrix.R, man/dgCMatrix-class.Rd,
1091              man/sparseMatrix-class.Rd: Don't need an "indicators" class - use the
1092              row names to store the levels - duh!  Added an example.
1093    
1094    2007-06-14  Martin Maechler  <maechler@stat.math.ethz.ch>
1095    
1096            * src/Csparse.c (Csparse_validate): check for *repeated* entries
1097            thanks to example from Christian Buchta; with a test here:
1098            * tests/simple.R:
1099    
1100    2007-06-07  Martin Maechler  <maechler@stat.math.ethz.ch>
1101    
1102            * R/Auxiliaries.R (callGeneric): another fix, needed for some cases
1103            of colSums(*, sparseResult = TRUE)
1104    
1105    2007-06-06  Martin Maechler  <maechler@stat.math.ethz.ch>
1106    
1107            * R/lsparseMatrix.R, R/ldenseMatrix.R (all, any): change default to
1108            'na.rm = FALSE' as "everywhere" else in R.
1109    
1110    2007-06-05 Douglas Bates <bates@stat.wisc.edu>
1111    
1112            * [r4421] src/CSparse_install.sh: Modify for new organization of
1113              CSparse package
1114            * [r4425] src/UFsparse_download.sh: Update to version 3.0.0 of
1115              SuiteSparse
1116            * [r4426] src/Makefile: add ./UFconfig to the include path for
1117              compilation
1118            * [r4427] src/cs.[ch]: update to CSparse version 2.2.0
1119            * [r4428] inst/doc/UFsparse/* src/{AMD,CHOLMOD,COLAMD}/*
1120              src/UFconfig/UFconfig.h: Update to version 3.0.0 of SuiteSparse
1121    
1122    2007-06-05  Martin Maechler  <maechler@stat.math.ethz.ch>
1123    
1124            * R/Auxiliaries.R (emptyColnames): + argument msg.if.not.empty, used in
1125            * R/sparseMatrix.R (prSpMatrix): now gives a message about
1126            suppressed column names.
1127    
1128    2007-06-04 17:13  Douglas Bates <bates@stat.wisc.edu>
1129    
1130            * [r4418] src/Csparse.c, src/HBMM.c, src/Mutils.c, src/Mutils.h,
1131              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dgCMatrix.c,
1132              src/dgeMatrix.c, src/dpoMatrix.c, src/dpoMatrix.h, src/dppMatrix.c,
1133              src/dppMatrix.h, src/dsCMatrix.c, src/dspMatrix.c, src/dspMatrix.h,
1134              src/dsyMatrix.c, src/dsyMatrix.h, src/dtpMatrix.c, src/dtrMatrix.c:
1135              Remove warnings after change to const char* CHAR
1136    
1137    2007-06-04 17:11  Douglas Bates <bates@stat.wisc.edu>
1138    
1139            * [r4417] inst/include/Matrix_stubs.c, inst/include/cholmod.h: Corrected
1140              type of M_cholmod_ssmult
1141    
1142    2007-06-03 14:42  Douglas Bates <bates@stat.wisc.edu>
1143    
1144            * [r4412] inst/include/Matrix_stubs.c, inst/include/cholmod.h,
1145              src/init.c: Yet another cholmod export - cholmod_ssmult
1146    
1147    2007-05-23  Martin Maechler  <maechler@stat.math.ethz.ch>
1148    
1149            * NAMESPACE: exported drop0(), since
1150            * man/drop0.Rd: I have seen several cases, I really wanted to use
1151            it, so our users may want too.
1152    
1153    2007-05-22  Martin Maechler  <maechler@stat.math.ethz.ch>
1154    
1155            * man/colSums.Rd: separately document colSums() etc, since these
1156            have the extra argument 'sparseResult'.
1157    
1158    2007-05-21  Martin Maechler  <maechler@stat.math.ethz.ch>
1159    
1160            * R/sparseMatrix.R (spMatrix): utility (T)sparse Matrix constructor;
1161            * man/spMatrix.Rd: docu., including examples
1162    
1163            * R/Auxiliaries.R (sp.colMeans): etc, using a patched callGeneric(),
1164            in order to make colMeans() etc fast *and* correct.
1165            * R/sparseVector.R (replSPvec): "[<-" functionality for
1166            sparseVectors; tested in
1167            * tests/simple.R:
1168    
1169    2007-05-19  Martin Maechler  <maechler@stat.math.ethz.ch>
1170    
1171            * R/sparseMatrix.R (print.sparseSummary): and summary() method for
1172            (very) sparse Matrices; output similar to Matlab's print().
1173    
1174    2007-05-17  Douglas Bates  <bates@stat.wisc.edu>
1175    
1176            * src/HBMM.c (Matrix_writeMatrixMarket): Write 1-based, not
1177            0-based, indices (Jose Quesada <quesada@gmail.com>).
1178    
1179    2007-05-16  Douglas Bates  <bates@stat.wisc.edu>
1180    
1181            * R/CHMfactor.R: Added solve methods for a CHMfactor object.
1182    
1183    2007-05-16  Martin Maechler  <maechler@stat.math.ethz.ch>
1184    
1185            * R/Auxiliaries.R (sparsapply): new utility, much faster than
1186            tapply1() for large sparse matrices.
1187    
1188    2007-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
1189    
1190            * R/Matrix.R (dim<-): reshape now via sparseVector.
1191    
1192            * R/sparseVector.R: methods and function for
1193            * R/AllClass.R: new "sparseVector" class and daughters.
1194            * NAMESPACE: export new classes
1195    
1196    2007-05-14  Martin Maechler  <maechler@stat.math.ethz.ch>
1197    
1198            * DESCRIPTION (Version): 0.99875-1
1199            * src/Makefile.win: also remove Lapack code from here (cf. 04-25).
1200    
1201    2007-05-11  Martin Maechler  <maechler@stat.math.ethz.ch>
1202    
1203            * R/Tsparse.R ([, Tsparse): fix last case: *duplicated*, symmetric
1204            indexing
1205            * tests/indexing.R: test set for that.
1206    
1207    2007-05-08  Martin Maechler  <maechler@stat.math.ethz.ch>
1208    
1209            * R/Tsparse.R (replTmat): fix the case of *duplicated* index
1210            entries.
1211            * tests/indexing.R(out): add regression test for it
1212    
1213    2007-04-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1214    
1215            * R/(l(dense|sparse))?Matrix.R (!): use 'x', not 'e1' as argument
1216            name for "!" method definitions.
1217    
1218    2007-04-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1219    
1220            * R/Tsparse.R (intI): new utility, used for "[" :
1221                    Cleanup up there, and fixes for duplicated indices - more TODO!
1222    
1223            * tests/indexing.R(out): more tests
1224    
1225    2007-04-25  Douglas Bates  <bates@stat.wisc.edu>
1226    
1227            * DESCRIPTION,src/Makefile: require R>= 2.5.0 and remove Lapack
1228            code that is now part of the R Lapack library.
1229    
1230            * src/init.c,inst/include/{Matrix_stubs.c,cholmod.h}:export
1231            cholmod_factorize_p (used in lme4 for GLMMs and NLMMs).
1232    
1233    2007-04-21  Martin Maechler  <maechler@stat.math.ethz.ch>
1234    
1235            * R/Matrix.R (image): method for all Matrices, not just sparse ones.
1236    
1237    2007-04-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1238    
1239            * R/Auxiliaries.R (tapply1): unname(.) -> colSums() etc don't end
1240            up with extraneous names '0'...'<n-1>'
1241    
1242    2007-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
1243    
1244            * R/dgTMatrix.R (mat2dgT): care about NAs
1245    
1246    2007-04-11  Martin Maechler  <maechler@stat.math.ethz.ch>
1247    
1248            * R/kronecker.R: triangularity preserving methods
1249    
1250    2007-03-27  Martin Maechler  <maechler@stat.math.ethz.ch>
1251    
1252            * R/kronecker.R: new file collecting kronecker() methods in one
1253                    place.  Goal: become much faster!
1254    
1255    2007-03-23  Martin Maechler  <maechler@stat.math.ethz.ch>
1256    
1257            * src/dtCMatrix.c (dtCMatrix_solve): use the new code from Kasper
1258            Kristensen based cs_spsolve() instead of _lsolve & _usolve which
1259            can be much faster.
1260    
1261            * tests/matprod.R: add regression tests for these (upper & lower).
1262    
1263    2007-03-19  Martin Maechler  <maechler@stat.math.ethz.ch>
1264    
1265            * R/Matrix.R (diff): method for our Matrices.
1266    
1267            * R/sparseMatrix.R (isDiagonal): check dim()!
1268    
1269    2007-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1270    
1271            * R/Matrix.R (dim<-): new method for "reshape()" built on a
1272            proposal from Tamas Papp.
1273    
1274    2007-03-16  Martin Maechler  <maechler@stat.math.ethz.ch>
1275    
1276            * R/AllGeneric.R: remove all  if(!isGeneric(.))  clauses
1277    
1278            * R/zzz.R (.onLoad, .onUnload): do *not* leave bind_activation(TRUE);
1279            rather define and export  cBind() and rBind() only.
1280            --> useRs *must* change code that used to have cbind()/rbind() !!
1281    
1282            * R/bind.R: change tests from cbind() to cBind() and similarly to rBind()
1283            * R/bind.Rout.save: ditto
1284    
1285    2007-02-16  Douglas Bates  <bates@r-project.org>
1286    
1287            * DESCRIPTION (Date, Version): 0.9975-11 with new date
1288            * src/dgCMatrix.c (R_to_CMatrix, compressed_to_TMatrix): remove
1289            const modifier on declaration of the array 'valid'
1290    
1291    2007-02-12  Douglas Bates  <bates@stat.wisc.edu>
1292    
1293            * R/CHMfactor.R: Add image method (coercion to sparseMatrix).
1294    
1295    2007-02-05  Martin Maechler  <maechler@stat.math.ethz.ch>
1296    
1297            * DESCRIPTION (Date, Version): 0.9975-10 with new date.
1298    
1299            * R/Ops.R (Arith): make sure Csparse o Csparse also works for e.g. ntCMatrix
1300            * tests/simple.R: test the above and some of these coercions:
1301    
1302            * R/nsparseMatrix.R: coercing "Csparse" to "lsparseMatrix";
1303                    be careful to avoid infinite recursion, using new coercions in
1304            * R/ngCMatrix.R and nsC... and ntC...
1305            * R/lsparseMatrix.R: ditto
1306    
1307            * R/SparseM-conv.R: more conversion, notably for triplet matrices.
1308    
1309            * src/dgCMatrix.c (R_to_C_Matrix): port Doug's fix and
1310            * R/Rsparse.R: reactivate .Call()s
1311    
1312            * tests/Class+Meth.R: a bit more on actual classes
1313    
1314    2007-02-04  Douglas Bates  <bates@stat.wisc.edu>
1315    
1316            * src/dgCMatrix.c (compressed_to_TMatrix): fix memory bug using strdup()
1317    
1318    2007-02-03  Martin Maechler  <maechler@stat.math.ethz.ch>
1319    
1320            * DESCRIPTION (Version): 0.9975-10 to upload
1321    
1322            * tests/Class+Meth.R (tstMatrixClass): require coercions to
1323            specific classes less unconditionally.
1324    
1325            * R/Auxiliaries.R: get rid of as_Tsparse() and as_Rsparse()
1326    
1327            * R/Tsparse.R (triu): etc, use as(*, "TsparseMatrix") instead of as_Tsparse()
1328    
1329            * R/Rsparse.R (.R.2.T): R-level workaround using compressed_to_TMatrix.
1330            * R/Rsparse.R (.R.2.C): R-level workaround since C-level
1331            R_to_CMatrix segfaults on one platform.
1332            Eliminate most coercion method to *specific* classes, and replace
1333            with virtual classes coercions.
1334    
1335    
1336    2007-02-01  Martin Maechler <maechler@stat.math.ethz.ch>
1337    
1338            * src/init.c: export the CHM...._validate() placeholders, since
1339            they *are* called.
1340    
1341            * tests/Class+Meth.R (classCanCoerce): and starting to test
1342            all as(<from>, <to>)
1343    
1344    2007-01-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1345    
1346            * R/Tsparse.R ([): more care when subsetting triangular Tsparse
1347            * tests/indexing.R: tested now
1348            * tests/indexing.Rout.save: updated
1349    
1350            * src/Csparse.c (Csparse_to_dense): use Rkind = -1 for PATTERN to
1351            * src/chm_common.c (chm_dense_to_SEXP): return "ngeMatrix" when
1352            appropriate.
1353    
1354            * NAMESPACE: export a trivial
1355            * R/Matrix.R: drop() Matrix-method
1356    
1357            * R/AllClass.R: moved all prototypes to virtual super classes.
1358    
1359            * R/Rsparse.R: many more coercions to have less exceptions in
1360            * tests/Class+Meth.R:
1361    
1362            * R/Ops.R (Compare): tweak for case with NA
1363            * tests/simpl.R: hence another 'FIXME' eliminated
1364    
1365    2007-01-29  Martin Maechler  <maechler@stat.math.ethz.ch>
1366    
1367            * R/diagMatrix.R (solve): the obvious methods for diagonalMatrix
1368            objects.
1369    
1370            * tests/Class+Meth.R (tstMatrixClass): now testing diag(), nnzero(),
1371              and more of "!", "&", "|", all, any; coercions
1372    
1373            * R/Rsparse.R: many coercions (which enable quite a few other
1374            methods), thanks to enhancements in
1375            * src/dgCMatrix.c (R_to_CMatrix): new, and
1376            * src/dgCMatrix.c (compressed_to_TMatrix): now for (d,l,n) ,
1377            symmetric & triangular and ..RMatrix objects.
1378    
1379            * src/TMatrix_as.c (Matrix_T_as_DENSE,Matrix_T_as_GENERAL):
1380            renamed file from src/dsTMatrix.c;
1381            now dealing with symmetric and triangular Tsparse coercions, both
1382            to dense and general.
1383    
1384    2007-01-27  Martin Maechler  <maechler@stat.math.ethz.ch>
1385    
1386            * src/dsTMatrix.c: has now "l" and "n" methods besides the "d" ones.
1387    
1388            * R/Ops.R (Arith): <dgCMatrix> o <numeric> now remains sparse
1389            where sensible when the <numeric> is of length > 1.
1390    
1391    2007-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1392    
1393            * R/Matrix.R ([<-): for M[] <- value: fix length
1394    
1395    2007-01-25  Martin Maechler  <maechler@stat.math.ethz.ch>
1396    
1397            * R/Auxiliaries.R (n2l_Matrix): new, to be used in
1398            * R/ndenseMatrix.R: new coercions n* -> l*
1399    
1400    2007-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
1401    
1402            * R/triangularMatrix.R: new file; simple triu() and tril() methods.
1403    
1404            * R/Ops.R ("Logic"): and other "Ops", many updates
1405    
1406    2007-01-18  Martin Maechler  <maechler@stat.math.ethz.ch>
1407    
1408            * src/Mutils.h (SET_DimNames): new utility
1409    
1410            * R/Auxiliaries.R (nnzero): improved and now exported via
1411    
1412            * NAMESPACE: + nnzero(); length() == prod(dim(.)) method for all "Matrix" objects
1413    
1414    2007-01-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1415    
1416            * R/diagMatrix.R (!): fix typo.
1417    
1418    2007-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
1419    
1420            * R/Auxiliaries.R (as_Csparse): and quite a few others:
1421                    allow to pass class definition --> speedup
1422            * R/sparseMatrix.R: apply the above
1423    
1424            * R/Csparse.R: coercion Csparse* to dense* now preserves shape properties.
1425    
1426            * src/Mutils.h (mMatrix_as_geMatrix): new, based on
1427            * src/Mutils.c (dup_mMatrix_as_geMatrix): new; generalization of
1428            old dup_mMatrix_as_dgeMatrix), eliminating a long-standing "FIXME".
1429    
1430            * src/dense.c (dense_to_Csparse): use new mMatrix_as_geMatrix()
1431    
1432            * R/denseMatrix.R (.dense2C): based on dense_to_Csparse: name it,
1433            and use it for "sparse*" as well, since it's faster than the
1434            as_Csparse(.) way.
1435    
1436    2007-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
1437    
1438            * R/Ops.R ("Logic"): more methods, notably an  <lgC> o <lgC> one.
1439    
1440    2007-01-12  Martin Maechler  <maechler@stat.math.ethz.ch>
1441    
1442            * R/Tsparse.R (.TM.repl.i.2col): new internal function to be used
1443            as method for   M[ ij ] <- v
1444            * R/Csparse.R:: go via Tsparse for "M[ij] <- v"
1445    
1446            * R/Ops.R: "Compare" for (C|R)sparse: need pointer slot for all
1447            FALSE answer
1448    
1449            * R/Csparse.R (replCmat): fix the "all non-zero" case with reordering
1450            * tests/indexing.R: test it, and some of the above
1451    
1452    2007-01-05  Martin Maechler  <maechler@stat.math.ethz.ch>
1453    
1454            * R/Auxiliaries.R (is_duplicatedT): new utility
1455    
1456  2007-01-05  Douglas Bates  <bates@stat.wisc.edu>  2007-01-05  Douglas Bates  <bates@stat.wisc.edu>
1457    
1458          * src/init.c (R_init_Matrix): export cholmod_scale          * src/init.c (R_init_Matrix): export cholmod_scale
1459    
1460    2006-12-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1461    
1462            * R/zzz.R (tmp): for R >= 2.5.0, extend formals of our
1463            base::as.matrix to (x, ...)
1464    
1465  2006-12-28  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-12-28  Martin Maechler  <maechler@stat.math.ethz.ch>
1466    
1467          * R/Ops.R ("Arith" etc): move almost all "Ops" methods to new R          * R/Ops.R ("Arith" etc): move almost all "Ops" methods to new R

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