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revision 2159, Sat Mar 29 08:09:05 2008 UTC revision 2257, Mon Sep 8 20:27:22 2008 UTC
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1    2008-09-08  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * DESCRIPTION (Version): 0.999375-14  to be released to CRAN,
4            in order to comply to to pending changes in R-devel (2.8.0).
5    
6    2008-09-05  Martin Maechler  <maechler@stat.math.ethz.ch>
7    
8            * R/Matrix.R (solve,..): use (Matrix,ANY)... instead of (Matrix,Matrix)
9            * R/Ops.R: ditto; most of these from John Chambers.
10            * man/Matrix-class.Rd
11    
12            * R/Auxiliaries.R (.diagU2N): fix for Rsparse*
13            * tests/Simple.R: test it
14    
15    2008-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>
16    
17            * man/drop0.Rd:
18            * R/Auxiliaries.R (drop0): new argument 'tol = 0' (and
19            'is.Csparse'); entails updates in
20            * R/Csparse.R, R/lMatrix.R, R/dMatrix.R
21    
22    2008-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
23    
24            * DESCRIPTION (Version): 0.999375-13 released to CRAN
25    
26    2008-08-29  Martin Maechler  <maechler@stat.math.ethz.ch>
27    
28            * R/Auxiliaries.R (attrSlotNames, attrSlots, attr.all_Mat): new
29            utilities, for now to be used in all.equal() methods.
30    
31            * R/Matrix.R (all.equal_Mat): be more careful (less tolerant) in
32            all.equal() methods.
33            * R/sparseMatrix.R: ditto
34    
35    2008-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
36    
37            * DESCRIPTION (Version): 0.999375-12 released to CRAN
38    
39            * R/Ops.R (Compare(<Csparse>,<Csparse>): fix for nsparseMatrix
40    
41    2008-08-27  Douglas Bates <bates@stat.wisc.edu>
42    
43            * R/sparseMatrix.R: fac2sparse() for NA's
44    
45    2008-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
46    
47            * R/sparseVector.R (all.equal.sparseV): make work for nsparseVector's
48    
49    2008-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
50    
51            * src/dgCMatrix.c (dgCMatrix_LU): partially revert change
52            r2175 (2008-04-23) and do give an error for a singular matrix.
53            * man/lu.Rd, R/Auxiliaries.R (detSparseLU): adapt to that.
54    
55            * R/LU.R: expand( <sparseLU> )
56    
57            * NAMESPACE, man/all.equal-methods.Rd:
58            * R/Matrix.R (all.equal): methods for Matrices,
59            * R/sparseMatrix.R, R/sparseVector.R: sparseMatrices and -Vectors
60    
61    
62    2008-08-23  Douglas Bates <bates@stat.wisc.edu>
63    
64            * [r2243] R/CHMfactor.R, man/CHMfactor-class.Rd: Added expand method and
65              documentation for CHMfactor class
66            * [r2241] R/CHMfactor.R: Added trivial coercion method for CHMfactor ->
67              pMatrix
68    
69    2008-08-19  Martin Maechler  <maechler@stat.math.ethz.ch>
70    
71            * R/nsCMatrix.R (setAs(., dgTMatrix))): remove unused method
72    
73    2008-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
74    
75            * R/Ops.R (.Ops2dge.via.x, and many others): eliminate never-used
76            variable assignments {from "next version" codetools}.
77            * R/Csparse.R, R/Tsparse.R: ditto
78    
79    2008-08-17  Martin Maechler  <maechler@stat.math.ethz.ch>
80    
81            * R/sparseVector.R (sp2vec, coerce to sparseVector):
82            make sure no integer overflows happen, and use double precision
83            (n, index) where appropriate.
84    
85            * tests/Simple.R: test "large" sparse vectors.
86    
87    2008-08-14  Martin Maechler  <maechler@stat.math.ethz.ch>
88    
89            * R/AllClass.R (sparseVector): 'length' and 'i' are "numeric", not
90            just integer (allowing much longer length).
91    
92    2008-07-28  Martin Maechler  <maechler@stat.math.ethz.ch>
93    
94            * R/AllClass.R (diagonalMatrix): extend  "sparseMatrix" instead of
95            "denseMatrix".  This renders "scarceMatrix" dispensable and
96            invalidates part of MM's presentations on "space of Matrix
97            classes", but seems cleaner overall.
98    
99            * R/diagMatrix.R, etc: eliminate "scarceMatrix", replacing it by
100            "sparseMatrix" in method signatures;
101            further, instead of coercing to "sparseMatrix", coerce to
102            "TsparseMatrix" now.
103    
104    2008-07-26  Martin Maechler  <maechler@stat.math.ethz.ch>
105    
106            * src/dgCMatrix.c (dgCMatrix_qrsol): allow third argument 'order' in
107            .Call(.)
108            * R/sparseMatrix.R (lm.fit.sparse), src/dgCMatrix.h, src/init.c: ditto
109    
110    2008-07-24  Martin Maechler  <maechler@stat.math.ethz.ch>
111    
112            * R/dgeMatrix.R: need solve(<dge>, <sparse>) against infinite
113            recursion in new test in
114            * tests/matprod.R: testing the above and another solve() case, below
115    
116            * R/sparseMatrix.R (lm.fit.sparse): slightly more efficient for
117            e.g. triangular 'x'.
118    
119            * src/dgCMatrix.c (dgCMatrix_qrsol): use AS_CSP() hence allowing dtC*
120            * src/dgCMatrix.c (dgCMatrix_cholsol): use AS_CHM_SP() to work
121            correctly with unit-triangular x
122    
123            * src/dsCMatrix.c (dsCMatrix_Csparse_solve): use AS_CHM_SP()
124            instead of not checking diagU.
125    
126            * R/diagMatrix.R, R/Auxiliaries.R: tweaks to allow later
127            experiments where diagonalMatrix would extend sparse*.
128    
129    
130    2008-07-23  Martin Maechler  <maechler@stat.math.ethz.ch>
131    
132            * src/dgCMatrix.c (compressed_non_0_ij): for nnzero(), use
133            "x@p[ncol(x)]" instead of length(x@i).
134            * R/Auxiliaries.R (nnzero): ditto
135    
136            * src/chm_common.c (as_cholmod_sparse): Do not use LENGTH(islot)
137            since that fails for over-allocated i.
138    
139            * tests/validObj.R: more testing of over-allocated (i,x) slots
140    
141    2008-07-23  Martin Maechler  <maechler@stat.math.ethz.ch>
142    
143            * src/chm_common.c (as_cholmod_sparse): Add 4th argument
144            'sort_in_place' and set it to TRUE in call from
145            * src/Csparse.c (Csparse_validate): sort in place, making sure that
146            validObject() continues sort the columns if needed.
147    
148            * tests/validObj.R: now tests that more thoroughly, and
149            * man/CsparseMatrix-class.Rd: documents it.
150    
151    2008-07-22  Douglas Bates <bates@stat.wisc.edu>
152    
153            * [r2233] src/chm_common.c: sort columns more carefully in
154              as_cholmod_sparse
155            * [r2231] src/chm_common.c: check for sorted columns in
156              as_cholmod_sparse instead of assuming it
157            * [r2228] src/cs_utils.c: Use R_alloc for semi-permanent storage when
158              expanding diagonal
159    
160    
161    2008-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
162    
163            * src/cs_utils.c (Matrix_as_cs): add check_Udiag switch
164            * src/cs_utils.h (AS_CSP & AS_CSP__): two versions
165            * src/dtCMatrix.c (dtCMatrix_sparse_solve): no longer needs
166            diagU2N().
167    
168            * R/diagMatrix.R (.sparseDiagonal): new utility, used in "old"
169            .spDiagonal() and new .trDiagonal().
170    
171            * R/dtCMatrix.R (solve): make use of .trDiagonal()
172    
173    2008-07-19  Martin Maechler  <maechler@stat.math.ethz.ch>
174    
175            * R/Auxiliaries.R (dimNamesCheck): fix very long standing buglet,
176            stumbled upon by Michael H.
177    
178            * tests/validObj.R: testing the bug-fix
179    
180            * src/chm_common.h (AS_CHM_SP__, AS_CHM_TR__): the non-diagU2N
181            versions.
182    
183            * src/chm_common.c (as_cholmod_sparse, as_cholmod_triplet): new
184            boolean argument 'check_Udiag' (formerly implicitly was FALSE).
185    
186            * src/Csparse.c (Csparse_Csparse_prod, ...): etc: use the new
187              AS_CHM_SP() which includes diagU2N.
188    
189            * inst/include/Matrix_stubs.c (M_as_cholmod_sparse): similarly
190            adapt to 3 arguments.
191    
192    2008-07-17  Douglas Bates <bates@stat.wisc.edu>
193    
194            * [r2220] src/dtCMatrix.c: Correct number of columns for rhs in
195              dtCMatrix_sparse_solve
196            * [r2219] src/cs_utils.c: eye->nz should be -1 for compressed column
197              storage
198            * [r2217] R/dtCMatrix.R, src/dtCMatrix.c, src/dtCMatrix.h, src/init.c:
199              Replace dtCMatrix_solve by more general dtCMatrix_sparse_solve and add
200              new solve method
201            * [r2216] src/cs_utils.c: Utility csp_eye in case we want to fold
202              Csparse_diagU2N functionality into Matrix_as_cs
203    
204    2008-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
205    
206            * inst/doc/factor2sparse.Rnw: revive a year-old unfinished vignette
207    
208    2008-07-16  Douglas Bates <bates@stat.wisc.edu>
209    
210            * [r2212] R/sparseMatrix.R: fac2sparse gets a drop.unused.levels
211              argument with default TRUE
212            * [r2211] inst/include/Matrix.h, inst/include/Matrix_stubs.c: Export
213              Csparse_diagU2N
214            * [r2210] R/dtCMatrix.R, man/dtCMatrix-class.Rd, src/dtCMatrix.c,
215              src/dtCMatrix.h, src/init.c: Remove vestigial methods based on the
216              parent array; new solve method for signature(a = "dtCMatrix", b =
217              "sparseMatrix")
218    
219    2008-07-14  Martin Maechler  <maechler@stat.math.ethz.ch>
220    
221            * R/diagMatrix.R (.bdiag): also keep result triangular
222    
223    2008-07-13  Douglas Bates <bates@stat.wisc.edu>
224    
225            * [r2208] src/dtCMatrix.c, src/dtTMatrix.c: Revise wording in error
226              messages
227    
228    2008-07-12  Martin Maechler  <maechler@stat.math.ethz.ch>
229    
230            * R/diagMatrix.R (.bdiag): make more sophisticated, keeping
231            symmetric- or nsparse-Matrix, also fixing the bug introduced with
232            the new version (.999375-10).
233    
234            * tests/Simple.R: regression test for the bugs.
235    
236    2008-07-07  Martin Maechler  <maechler@stat.math.ethz.ch>
237    
238            * R/sparseVector.R (spV2M): fix for "isparseVector".
239            Further, fix <diag> -> <sparseVector> coercion
240            (repSpV): add rep(<sparseVector>, .) method
241    
242            * R/sparseMatrix.R ([<-): when the RHS is a "scarce"Matrix, do *not*
243            use as.vector(.).
244    
245            * R/Tsparse.R ([<-): & [CR]sparse.R: methods for value = "sparseVector"
246    
247            * R/AllClass.R: new (hidden) class union "scarceMatrix"
248            * R/AllClass.R: sparseVector: add prototype
249    
250            * src/dsCMatrix.c (chk_nm): fix "Cholesky" check, thanks to
251            Kasper Kristensen
252    
253    2008-06-28  Martin Maechler  <maechler@stat.math.ethz.ch>
254    
255            * tests/other-pkgs.R: add more interesting Matrix -> graph
256    
257    2008-06-27  Martin Maechler  <maechler@stat.math.ethz.ch>
258    
259            * R/sparseMatrix.R (Tsp2grNEL): add 'need.uniq' argument for speed
260            improvement in "[CR]sparseMatrix" -> "graphNEL" coercion.
261    
262    2008-06-25  Martin Maechler  <maechler@stat.math.ethz.ch>
263    
264            * DESCRIPTION: release 0.999375-10 to CRAN
265    
266            * R/diagMatrix.R (.bdiag): use more efficient Bates-algorithm for
267            .bdiag().
268            * man/bdiag.Rd: update, including test.
269    
270    2008-06-24  Martin Maechler  <maechler@stat.math.ethz.ch>
271    
272            * tests/Simple.R: add minimal bdiag() checks
273    
274            * R/diagMatrix.R (bdiag): fix bdiag(diag(4:5)) case;
275              factor out the Tsparse - internal computation into new .bdiag()
276    
277    2008-06-14  Martin Maechler  <maechler@stat.math.ethz.ch>
278    
279            * R/nsparseMatrix.R: specific fast all() and any() methods.
280    
281            * src/dgTMatrix.c (MAKE_gTMatrix_to_geMatrix): better error message
282            when trying to produce too large result.
283    
284            * inst/test-tools.R (checkMatrix): add 'do.matrix' with a check for
285            very large matrices.
286    
287            * R/sparseMatrix.R (printSpMatrix2): new function, used by
288            show(<sparseMatrix>).
289    
290            * R/diagMatrix.R (show): print only diagonal entries when nrow(.) >= 50.
291    
292    2008-06-13  Martin Maechler  <maechler@stat.math.ethz.ch>
293    
294            * src/Mutils.c (m_encodeInd, m_encodeInd2):
295            * R/*.R: .Call(m_encodeInd2?, ..) instead of encodeInd2?(..).
296    
297            * R/Auxiliaries.R (encodeInd2?): care against integer overflow (for
298            big matrices): -> 2nd argument 'di' instead of 'nr' !
299    
300    2008-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
301    
302            * R/dtCMatrix.R: faster dgC* -> dtC* method
303            * tests/Simple.R: (hence removed "FIXME")
304    
305            * R/Auxiliaries.R (copyClass): add 'check = .copyClass.check'
306            which can be be turned off for possible speed gains.
307    
308    2008-06-02  Martin Maechler  <maechler@stat.math.ethz.ch>
309    
310            * R/dMatrix.R, R/Tsparse.R: get rid of some disambiguation warnings
311    
312            * R/not.R: fix !<ldiMatrix>
313            implement two old "FIXME"s:  !<ldenseMatrix> & !<ndenseMatrix>
314    
315            * R/diagMatrix.R (Ops): fix one-off thinko in
316            <diagonal> o <numeric> methods
317    
318            * inst/test-tools.R: checkMatrix(): drop0(m12) unconditionally
319    
320    2008-05-30  Martin Maechler  <maechler@stat.math.ethz.ch>
321    
322            * R/diagMatrix.R (Ops): more <diagonal> o <Matrix> methods
323            * tests/Simple.R: testing the above
324    
325    2008-05-07  Martin Maechler  <maechler@stat.math.ethz.ch>
326    
327            * NAMESPACE: also import "Ops" {found via new tools:::get_S4_generics_with_methods()}
328    
329    2008-05-03  Martin Maechler  <maechler@stat.math.ethz.ch>
330    
331            * R/Matrix.R (dimnames<-): dimnames(.) <- NULL works with a message;
332            * NAMESPACE (unname): finally exported
333    
334    2008-04-28  Martin Maechler  <maechler@stat.math.ethz.ch>
335    
336            * R/Auxiliaries.R (cholMat): possibly keep packed
337    
338            * inst/test-tools.R (checkMatrix): add fixed determinant.matrix()
339            for R < 2.7.0.
340    
341            * R/Tsparse.R ([): for triangularMatrix, check if result may be
342            triangular.
343            * tests/indexing.R: regression test
344    
345    2008-04-26  Martin Maechler  <maechler@stat.math.ethz.ch>
346    
347            * inst/test-tools.R (checkMatrix): test <Ops> not only for dMatrix
348            * R/Ops.R: more methods, for lMatrix/nMatrix
349    
350    2008-04-24  Martin Maechler  <maechler@stat.math.ethz.ch>
351    
352            * R/expm.R: new file for all expm() methods; notably new ones for
353            diagonal*, triangular*, symmetric* and also simple "matrix".
354    
355    2008-04-23  Martin Maechler  <maechler@stat.math.ethz.ch>
356    
357            * R/dsyMatrix.R: setAs(.) rather than setIs(.)  "to dpoMatrix"
358    
359            * inst/test-tools.R (assert.EQ.mat): better message when not equal
360    
361            * src/dgeMatrix.c (dgeMatrix_matrix_crossprod): allow integer RHS.
362    
363            * R/AllClass.R (ddiMatrix,ldiMatrix): extend [dl]Matrix instead of
364            [dl]denseMatrix {identical slots; but more logical method dispatch}
365    
366    2008-04-23  Martin Maechler  <maechler@stat.math.ethz.ch>
367    
368            * R/sparseMatrix.R (summary): use length(<i-slot>) instead of nnzero()
369    
370            * R/diagMatrix.R (determinant): method
371    
372    2008-04-22  Martin Maechler  <maechler@stat.math.ethz.ch>
373    
374            * src/dsCMatrix.c (dsCMatrix_Cholesky): suppress CHOLMOD printing too
375    
376            * R/Rsparse.R (.viaC.to.R): uplo fix for symmetric & triangular
377    
378            * R/dsCMatrix.R (determinant): switch to use Cholesky( 'LDL' ) and
379            its diagonal
380    
381    2008-04-21  Martin Maechler  <maechler@stat.math.ethz.ch>
382    
383            * R/dMatrix.R (Summary): short-cut for prod(<sparse>)
384    
385            * R/not.R: fix !<"U"-diag-ltrMatrix> ; drop {R < 2.6.0}-branch
386    
387            * R/Auxiliaries.R (tT2gT): fix for "U"-diag-ltTMatrix
388    
389            * R/AllClass.R: ltTMatrix validity: call (more stringent) tTMatrix_validate
390    
391    2008-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
392    
393            * R/Ops.R (Ops.x.x): aux.function, not just for (dMatrix,dMatrix)
394    
395            * R/Ops.R (.do.Logic.lsparse): fix NA case
396    
397            * R/Tsparse.R (replTmat): fix r.sym case, using indTri()
398    
399            * R/Auxiliaries.R (nnzero): fix special cases, using
400            * R/Auxiliaries.R (indDiag): new utility
401            * R/Auxiliaries.R (indTri): new argument 'diag'
402    
403            * R/dMatrix.R: Summmary(<ddenseMatrix>): different branch for dsy*
404    
405    2008-04-18  Martin Maechler  <maechler@stat.math.ethz.ch>
406    
407            * R/diagMatrix.R: "Summary" methods, and more "Arith" / "Ops"
408    
409            * src/Csparse.c (Csparse_drop): preserve (uplo,diag) for
410            ".tCMatrix" triangular matrix.
411    
412            * R/Auxiliaries.R (drop0): use diagU2N(); according to helpfile,
413            'clx' can be class *or* class representation.
414            (nnzSparse): new.
415            (non0ind): new 'xtendSymm' argument; used in
416            * R/Ops.R:
417    
418            * R/pMatrix.R: more efficient determinant() method
419    
420    2008-04-17  Martin Maechler  <maechler@stat.math.ethz.ch>
421    
422            * [disactivated] R/Matrix.R (det): det() as base::det(), but with Matrix environment
423            * [disactivated] NAMESPACE: export(det)
424    
425            * R/diagMatrix.R (mkDiag): new substitute for diag()
426    
427            * R/Auxiliaries.R (nnzero): fix for "diagU2N"-case
428            (as0, as1): new utility.
429    
430            * R/Csparse.R (diag, band): need diagU2N()
431    
432            * src/dgeMatrix.c (get_norm): return NA when 'x' slot has NA/NaN.
433    
434            * R/lMatrix.R: coerce(nMatrix |-> lMatrix) fix
435    
436            * R/Ops.R (Compare): fix <nsp> o <nsp> case
437    
438            * R/nsparseMatrix.R, R/pMatrix.R: is.na() method
439    
440    2008-04-16  Martin Maechler  <maechler@stat.math.ethz.ch>
441    
442            * R/Auxiliaries.R (signPerm): new utility for
443            * R/Auxiliaries.R (detSparseLU): determinant() via sparseLU
444    
445            * src/dsCMatrix.c (dsCMatrix_LDL_D): suppress 'CHOLMOD warning';
446            since we have our own error handler (and can use tryCatch() from R).
447    
448    2008-04-15  Martin Maechler  <maechler@stat.math.ethz.ch>
449    
450            * R/dgTMatrix.R (image): ha! set col=NA if lwd is small -- very nice!
451    
452            * R/dsCMatrix.R (determinant): use tryCatch() and switch to lu()
453            when not positive definite.
454    
455            * R/Auxiliaries.R (asTri): new auxiliary
456            (non0.i): make *much* faster for Tsparse with many non-zero
457            entries; add 'uniqT = TRUE' argument to be used when sorting is undesired.
458    
459            * tests/Class+Meth.R (dotestMat): now build on checkMatrix() from
460            test-tools.R , see below
461    
462            * R/dMatrix.R: fix "Summary" method: + diagU2N()
463    
464            * NAMESPACE, R/Matrix.R: add mean() method
465    
466    2008-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
467    
468            * R/dgTMatrix.R (image): allow to *not* take abs(), and use
469            cold-hot colors; try *changed* default useAbs = FALSE
470            * man/image-methods.Rd:  nice examples
471    
472    2008-04-11  Martin Maechler  <maechler@stat.math.ethz.ch>
473    
474            * inst/test-tools.R (checkMatrix): new function for modularizing part
475            of tstMatrixClass() in tests/Class+Meth.R
476    
477            * R/dsCMatrix.R: coercion from "matrix"
478            * R/ltTMatrix.R, R/ntTMatrix.R: ditto (change it).
479    
480            * tests/Class+Meth.R (tstMatrixClass): some cleanup;
481            add test for as(matrix(,0,0), <class>)
482    
483    2008-04-09  Martin Maechler  <maechler@stat.math.ethz.ch>
484    
485            * src/dgeMatrix.c (dgeMatrix_determinant): for n == 0,
486            work as determinant(matrix(,0,0)).
487    
488            * src/dgCMatrix.c (dgCMatrix_LU): return {L,U} as dtCMatrix
489            * man/sparseLU-class.Rd: ditto
490    
491            * R/dgCMatrix.R (determinant): method building on lu()
492            * R/sparseMatrix.R, Matrix.R, ...: ditto
493    
494            * R/Auxiliaries.R (mkDet): auxiliary for determinant()
495    
496    2008-04-07  Martin Maechler  <maechler@stat.math.ethz.ch>
497    
498            * R/sparseMatrix.R (summary<sparseMatrix>): no 'x' column for
499            pattern matrices.
500    
501    2008-04-02  Martin Maechler  <maechler@stat.math.ethz.ch>
502    
503            * src/dense.c (dense_to_Csparse): all declarations *before*
504            R_CheckStack(); needed e.g. for ancient gcc 2.96.
505    
506    
507  2008-03-29  Martin Maechler  <maechler@stat.math.ethz.ch>  2008-03-29  Martin Maechler  <maechler@stat.math.ethz.ch>
508    
509          * DESCRIPTION (Version): 0.999375-9 --- need to release          * DESCRIPTION (Version): 0.999375-9 --- need to release
510          for R-devel (and R 2.7.0 alpha soon).          for R-devel (and R 2.7.0 alpha soon).
511    
512            * R/AllClass.R: drop "double" from "atomicVector" class union
513    
514            * R/AllGeneric.R (rcond): check for base::rcond instead of R version
515            * R/dgeMatrix.R: ditto
516    
517          * R/sparseMatrix.R (summary): count NAs          * R/sparseMatrix.R (summary): count NAs
518    
519            * inst/doc/Intro2Matrix.Rnw: changes, aim for *one* introduction.
520    
521  2008-03-28  Martin Maechler  <maechler@stat.math.ethz.ch>  2008-03-28  Martin Maechler  <maechler@stat.math.ethz.ch>
522    
523          * R/AllGeneric.R: rcond(., norm) instead of rcond(., type), in          * R/AllGeneric.R: rcond(., norm) instead of rcond(., type), in

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