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revision 1368, Sat Aug 12 17:34:00 2006 UTC revision 1673, Mon Nov 6 20:54:26 2006 UTC
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1    2006-11-06  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * R/Csparse.R (replCmat): symmetric indexing of symmetric matrix
4            now returns symmetric.
5    
6            * R/zzz.R ("diag<-"): replace "diag<-" in base for R <= 2.4.x
7    
8            * R/Matrix.R (.M.sub.i.2col):  new, for  M[ cbind(i,j) ] indexing.
9            * R/Matrix.R (.M.repl.i.2col): new, for  M[ cbind(i,j) ] <- value
10    
11            * R/Auxiliaries.R (.type.kind): added
12    
13    2006-11-04  Martin Maechler  <maechler@stat.math.ethz.ch>
14    
15            * src/cs.[ch]: updated to CSparse Version 2.0.3 by simply
16            running src/CSparse_install.sh
17    
18            * R/denseMatrix.R: "[": keep symmetric on symmetric indexing.
19    
20    2006-11-03  Martin Maechler  <maechler@stat.math.ethz.ch>
21    
22            * src/dsCMatrix.c (dsCMatrix_Csparse_solve): new
23            * R/dsCMatrix.R (solve): "fully-sparse" using the above.
24    
25            * R/AllClass.R: "pMatrix" now also inherits from "generalMatrix"
26    
27            * tests/Class+Meth.R (tstMatrixClass): now assure
28            the (important in method programming) property :
29    
30                    ###>>  Every "Matrix" is either
31                    ###>>  "general*", "symmetric*", "triangular*" or "diagonal*"
32    
33                    (where "*" stands for "Matrix")
34    
35            * R/Auxiliaries.R (diagU2N): now .Call()s Csparse_diagU2N for <Csparse>
36    
37            * R/dMatrix.R (Compare(<dMatrix>,<dMatrix>): update and
38            * tests/validObj.R: checks for "comparison"
39    
40            * R/sparseMatrix.R ([): improved indexing for sparse;
41                    trying to keep <symmetric>[ n, n] symmmetric
42    
43            * tests/indexing.R: indexing for logical sparse now ok
44    
45    
46    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
47    
48            * src/Tsparse.c: use xTsparse_validate() , and hence remove
49    
50            * src/{ltC,lsC,lgT}Matrix.[ch]: removed
51    
52    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
53    
54            * R/AllClass.R (Matrix-class): check length of dimnames in validity.
55    
56            * tests/simple.R: validObject() checking the above.
57    
58            * src/dgCMatrix.c (xCMatrix_validate): new, small and simple,
59            replacing both dgCMatrix_validate and lgCM*.
60    
61            * src/Csparse.c (Csparse_dense_prod, etc): do not lose dimnames;
62            fix dimnames setting in other places.
63            * src/chm_common.c (chm_dense_to_SEXP): now can pass dimnames
64    
65    2006-11-01  Martin Maechler  <maechler@stat.math.ethz.ch>
66    
67            * R/Csparse.R,src/Csparse.c, etc: tcrossprod(<CsparseM>,<CsparseM>)
68    
69            * R/sparseMatrix.R (isSymmetric): drop 'factors' slot for
70            symmetry test, via
71            * R/Auxiliaries.R (.as.dgC.0.factors):
72    
73    2006-11-01  Douglas Bates  <bates@r-project.org>
74    
75            * R/Csparse.R,src/Csparse.c,tests/matprod.R,
76            man/CsparseMatrix-class.Rd: crossprod(<CsparseMatrix>,
77            <CsparseMatrix>) added
78    
79    2006-10-30  Martin Maechler  <maechler@stat.math.ethz.ch>
80    
81            * tests/matprod.R: add a variation of Harri's example
82    
83            * R/dsparseMatrix.R: fix crossprod(<dsparse>, <dge>) to *not*
84            recursive infinitely.
85    
86            * R/dgCMatrix.R: + solve(<sparse>, <sparse>)
87    
88            * tests/indexing.R: add test for the "<" bug fixed 10-27 in R/dMatrix.R
89    
90    2006-10-28  Martin Maechler  <maechler@stat.math.ethz.ch>
91    
92            * tests/Class+Meth.R (tstMatrixClass): more: use non-trivial
93            matrix if possible; test m+m == 2*m; now test dgRMatrix.
94            * R/dgRMatrix.R (.to.dgR): a few more coercions, in order to
95            satisfy the above test.
96    
97    2006-10-27  Martin Maechler  <maechler@stat.math.ethz.ch>
98    
99            * R/Matrix.R (Ops):  <Matrix> o <matrix>  method added
100    
101            * R/dgCMatrix.R: solve(a, b="missing") based on
102            * src/dgCMatrix.c (dgCMatrix_matrix_solve): extend to work with
103            RHS = NULL.
104    
105            * R/diagMatrix.R (diagdiagprod): extend %*% etc to ldiMatrix;
106            add more (needed) [t]crossprod() methods.
107    
108            * man/ddiMatrix-class.Rd: more info, notably on 'diag'
109    
110            * R/Auxiliaries.R (as_CspClass): cleanup
111            (drop0): internal utility for "Csparse_drop(*, 0)"
112            (.bail.out.2): encourage active feedback
113    
114    2006-10-26  Martin Maechler  <maechler@stat.math.ethz.ch>
115    
116            * R/dMatrix.R(Compare): new(), then slots [no validity check]
117    
118            * src/Csparse.c (Csparse_validate): fixed (and more efficient in
119            non-valid or 'sorted' case).
120    
121            * R/dsparseMatrix.R: add "chol" method.
122            * R/ddenseMatrix.R: ditto
123    
124            * R/diagMatrix.R (Ops): group methods for  <diagonal> o <sparse>
125            * NAMESPACE (Ops)
126            * R/diagMatrix.R (diag2T): simple utility used "higher level"
127            coercion; deprecating direct lower level coercions.
128    
129            * R/*.R (seq): use seq_len() and seq_along() where possible.
130    
131    
132    2006-10-23  Martin Maechler  <maechler@stat.math.ethz.ch>
133    
134            * DESCRIPTION (Version): 0.9975-5 ready for release
135    
136    2006-10-20  Douglas Bates  <bates@stat.wisc.edu>
137    
138            * src/init.c (R_init_Matrix): export more cholmod CCallable functions.
139    
140    2006-10-20  Martin Maechler  <maechler@stat.math.ethz.ch>
141    
142            * R/AllClass.R (corMatrix): add 'validity' check;
143                    comment out unused "LDL" class definition
144            * NAMESPACE: mention, but do not export "LDL" class
145            * R/corMatrix.R: new (simple), needed for R-devel with
146            * tests/Class+Meth.R (tstMatrixClass): 1 exception for corMatrix
147              coerce and t() exceptions for all 5 'Mat.MatFact' classes.
148    
149    2006-10-19  Douglas Bates  <bates@stat.wisc.edu>
150    
151            * src/chm_common.h: Add R_cholmod_start to initialize cholmod to
152            use Rprintf and R's error handling.
153    
154    2006-10-17  Martin Maechler  <maechler@stat.math.ethz.ch>
155    
156            * R/diagMatrix.R (%*%): rep(*, each = .) in Matrix %*% diagonal.
157            * tests/matprod.R: add tests for the bug fixed.
158    
159    2006-10-11  Douglas Bates  <bates@stat.wisc.edu>
160    
161            * src/HBMM.[ch]: remove HarwellBoeing format for writing.
162            * src/SOURCES_C.mkf (SOURCES_C): no longer compile iohb.c
163    
164    2006-10-06  Douglas Bates  <bates@stat.wisc.edu>
165    
166            * R/d[gs]CMatrix.R: deprecate the writeHB function.  Use writeMM instead.
167    
168    2006-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
169    
170            * DESCRIPTION (Version): 0.9975-3
171    
172            * R/diagMatrix.R (bdiag): new function constructing block diagonal
173            (sparse) matrices.
174            * man/bdiag.Rd: docu + examples
175    
176            * R/Csparse.R (replCmat): calling new Csparse_drop() now.
177    
178            * src/Csparse.c (Csparse_general_to_symmetric, Csparse_drop): new functions
179            * R/lsCMatrix.R: three more coercions to lsC (thanks to the above)
180    
181            * R/diagMatrix.R (Diagonal): '[<-' method for diag.matrices such
182            that result is sparse or diagonal (and not dense).
183    
184            * man/Subassign-methods.Rd: fix examples
185    
186            * R/Matrix.R (Matrix):  Matrix(0, *) or Matrix(*, sparse=TRUE)
187            should always return a sparse (and not sometimes a diagonal) matrix.
188    
189    2006-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
190    
191            * R/Matrix.R ([<-): also for value "Matrix" or "matrix"
192    
193    2006-10-04  Douglas Bates  <bates@stat.wisc.edu>
194    
195            * DESCRIPTION (Version): 0.9975-2
196    
197            * inst/include/Matrix_stubs.c (M_cholmod_sparse_to_triplet): export more symbols
198    
199    2006-10-02  Douglas Bates  <bates@R-project.org>
200    
201            * tests/dg_Matrix.R: Simplify test taking into account new code.
202    
203    2006-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
204    
205            * R/Csparse.R (replCmat): improve for missing i / j in non-simple cases
206    
207            * R/lsTMatrix.R: new files w/ missing methods
208            * R/nsTMatrix.R:  "  'for completeness'
209    
210            * tests/Class+Meth.R: a bit less 'not.ok.classes'
211    
212            * R/Tsparse.R (t): generalized "t" method from "dgT*" to "Tsparse*"
213    
214    
215    2006-09-28  Douglas Bates  <bates@R-project.org>
216    
217            * src/dppMatrix.h: Ensure definition of dspMatrix_validate is
218            included.
219    
220            * src/init.c, inst/include/{Matrix.h,Matrix_stubs.h,cholmod.h}:
221            Export C-callable functions used in Zt_create in lme4.
222    
223    2006-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
224    
225            * DESCRIPTION (Version): 0.9975-1
226    
227            * tests/simple.R: less checks fail; using NA, found that our
228                    kronecker() is not base-compatible with NA's.
229    
230            * R/dMatrix.R: "Compare" method now implemented for all cases
231    
232            * R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility
233    
234            * man/dtpMatrix-class.Rd: mention length of 'x' slot
235    
236            * src/dtpMatrix.c (dtpMatrix_validate): fix check
237            * src/dspMatrix.c (dspMatrix_validate): ditto
238    
239            * R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
240              including coercion to [nl]tTMatrix.
241    
242            * R/diagMatrix.R (show): print a header line as for other classes.
243    
244    2006-09-27  Martin Maechler  <maechler@stat.math.ethz.ch>
245    
246            * src/Makefile.win (SUBDIRS): fix typo
247    
248    2006-09-19  Martin Maechler  <maechler@stat.math.ethz.ch>
249    
250            * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
251    
252    2006-09-18  Douglas Bates  <bates@stat.wisc.edu>
253    
254            * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
255            symmetric and y missing in R code using %*% (cholmod_aat doesn't
256            accept a symmetric matrix).
257            * tests/group-methods.R: Uncomment test of crossprod applied to
258            lsCMatrix objects.
259    
260    2006-09-18  Martin Maechler  <maechler@stat.math.ethz.ch>
261    
262            * R/AllClass.R (symmetricMatrix): add validity method (available
263            in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
264    
265            * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
266    
267            * tests/indexing.Rout.save:
268            * tests/indexing.R: additions, mainly for 'lsparse'
269    
270            * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
271            case.
272    
273            * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
274    
275    2006-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
276    
277            * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
278                    as 'N' (1-letter - Ok?)
279    
280            * tests/group-methods.R: add test for logical + NAs
281    
282            * R/dMatrix.R ("Compare"): fix to work with NA's
283    
284            * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
285    
286            * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
287                    which is implemented.
288    
289    2006-09-15  Martin Maechler  <maechler@stat.math.ethz.ch>
290    
291            * src/chm_common.c: coerce logical <-> double instead of
292            typecasting;  needed for "l" matrix handling in cholmod.
293    
294            * tests/other-pkgs.R (graph): small extension in "graph" checks.
295    
296            * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
297            (Tsp2grNEL): other fixes needed
298    
299    2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
300    
301            * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
302                    Matrices, since "lMatrix", also "lsparseM" can have NA
303            * R/ndenseMatrix.R, etc: new source files
304            * man/nsparseMatrix-classes.Rd, etc: new help files
305            * tests/: adaptions
306            * src/chm_common.c (chm_dense_to_SEXP): and others:
307                    new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
308            * src/Csparse.c, etc: ditto
309    
310    2006-09-11  Douglas Bates  <bates@R-project.org>
311    
312            * src/Mutils.[ch],init.c inst/include/*.h: Move the
313            alloc_d**Matrix functions to the lme4 package.
314    
315    2006-09-09  Douglas Bates  <bates@R-project.org>
316    
317            * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
318            fixed
319    
320    2006-09-09  Martin Maechler  <maechler@stat.math.ethz.ch>
321    
322            * R/lMatrix.R: new
323    
324            * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
325    
326            * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
327            * man/tcrossprod.Rd: ditto
328    
329    2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
330    
331            * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
332            for exported functions
333            * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
334            Remove partitioning algorithms for sparse matrix reordering.  The
335            copyright on the Metis code was problematic and the methods were
336            rarely used.
337            * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
338            operations are now done entirely in CHOLMOD code.
339    
340    2006-09-06  Douglas Bates  <bates@R-project.org>
341    
342            * src/Mutils.h: Remove functions that are no longer used.
343    
344    2006-09-04  Douglas Bates  <bates@R-project.org>
345    
346            * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
347            * src/DEPS.mkf: update
348    
349    2006-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>
350    
351            * created branches/Matrix-for-R-2.3.x;  on trunk: do
352            * DESCRIPTION (Version): 0.9975-0
353            (Depends): R (>= 2.4.0)
354    
355    2006-09-01  Douglas Bates  <bates@R-project.org>
356    
357            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
358    
359    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
360    
361            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
362            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
363    
364            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
365    
366    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
367    
368            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
369            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
370            * R/dsparseMatrix.R: ditto
371            * R/Csparse.R: ditto
372    
373    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
374    
375            * R/dMatrix.R (Compare): improve availability of "<", etc
376            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
377    
378    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
379    
380            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
381            of a 0-index which was used as 1-index (..hmm)
382    
383            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
384    
385            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
386            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
387            (.is.diagonal): ditto
388    
389            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
390    
391            * R/Matrix.R (Matrix): also work for NA data
392    
393    2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
394    
395            * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
396            in all cases.
397    
398    2006-08-27  Douglas Bates  <bates@R-project.org>
399    
400            * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
401            (ddense_band): Added triu, tril and band for ddenseMatrix objects.
402    
403    2006-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
404    
405            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
406            subclasses of "ddenseMatrix"
407            * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
408            * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
409            instead of half dozen specialized ones.
410    
411    2006-08-25  Douglas Bates  <bates@R-project.org>
412    
413            * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
414            <tillard@cirad.fr> - ordering standard errors to match effects.
415    
416    2006-08-24  Douglas Bates  <bates@R-project.org>
417    
418            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
419            on R_ldl.
420            * R/lCholCMatrix.R,
421            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
422            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
423            * many files in ./R and ./src: Use more general version of
424            dup_mMatrix_as_dgeMatrix to simplify method definitions.
425            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
426            dtpMatrix, dspMatrix and dppMatrix conversions.
427    
428    
429    2006-08-23  Douglas Bates  <bates@R-project.org>
430    
431            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
432            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
433            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
434            dgeMatrix_crossprod (may need to do this in other places).
435            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
436            generic and method for dsCMatrix.  Use CHOLMOD for chol().
437    
438    2006-08-22  Douglas Bates  <bates@R-project.org>
439    
440            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
441            types of classed Matrices, matrices or numeric or logical vectors.
442            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
443            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
444            to Mutils.h (as an inline) and change name to Matrix_check_class;
445            fixes in as_cholmod_factor and chm_factor_to_SEXP.
446            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
447            dsCMatrix_matrix_solve.  Comment out vestigial functions.
448            * src/Csparse.c: use diag_P and uplo_P macros.
449    
450    2006-08-21  Douglas Bates  <bates@R-project.org>
451    
452            * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
453            valgrind.
454            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
455            inverses.
456            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
457            -Wall warnings.
458            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
459            Use dup_mMatrix_as_dgeMatrix.
460    
461    2006-08-20  Douglas Bates  <bates@R-project.org>
462    
463            * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
464            * tests/sparseQR.R: Added
465            * man/sparseQR-class.Rd: Document methods for qr.* generics
466            * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
467    
468    2006-08-19  Douglas Bates  <bates@R-project.org>
469    
470            * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
471            Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
472            and qr.fitted.
473            * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
474            * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
475    
476    2006-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
477    
478            * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
479            the base version has no "..." argument.
480    
481            * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
482    
483            * R/Matrix.R: define and
484            * NAMESPACE: export as.numeric() and as.logical() methods.
485                    Let's hope these do not badly slow down something...
486            Finally export the zapsmall() method.
487    
488    2006-08-17  Douglas Bates  <bates@R-project.org>
489    
490            * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
491            R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
492            * src/dtCMatrix.c :Remove code that is no longer used
493            * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
494    
495    2006-08-14  Douglas Bates  <bates@R-project.org>
496    
497            * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
498            Csparse_to_logical and Csparse_symmetric_to_general.
499            * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
500            coercion methods between CsparseMatrix and TsparseMatrix.
501    
502    2006-08-14  Douglas Bates  <bates@R-project.org>
503    
504            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
505            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
506            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
507            possible.
508    
509  2006-08-12  Douglas Bates  <bates@R-project.org>  2006-08-12  Douglas Bates  <bates@R-project.org>
510    
511          * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,          * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,

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