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revision 1312, Thu Jul 6 15:29:56 2006 UTC revision 1571, Sat Sep 16 21:03:12 2006 UTC
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1    2006-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * tests/group-methods.R: add test for logical + NAs
4    
5            * R/dMatrix.R ("Compare"): fix to work with NA's
6    
7            * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
8    
9            * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
10                    which is implemented.
11    
12    2006-09-15  Martin Maechler  <maechler@stat.math.ethz.ch>
13    
14            * src/chm_common.c: coerce logical <-> double instead of
15            typecasting;  needed for "l" matrix handling in cholmod.
16    
17            * tests/other-pkgs.R (graph): small extension in "graph" checks.
18    
19            * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
20            (Tsp2grNEL): other fixes needed
21    
22    2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
23    
24            * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
25                    Matrices, since "lMatrix", also "lsparseM" can have NA
26            * R/ndenseMatrix.R, etc: new source files
27            * man/nsparseMatrix-classes.Rd, etc: new help files
28            * tests/: adaptions
29            * src/chm_common.c (chm_dense_to_SEXP): and others:
30                    new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
31            * src/Csparse.c, etc: dito
32    
33    2006-09-11  Douglas Bates  <bates@R-project.org>
34    
35            * src/Mutils.[ch],init.c inst/include/*.h: Move the
36            alloc_d**Matrix functions to the lme4 package.
37    
38    2006-09-09  Douglas Bates  <bates@R-project.org>
39    
40            * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
41            fixed
42    
43    2006-09-09  Martin Maechler  <maechler@stat.math.ethz.ch>
44    
45            * R/lMatrix.R: new
46    
47            * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
48    
49            * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
50            * man/tcrossprod.Rd: dito
51    
52    2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
53    
54            * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
55            for exported functions
56            * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
57            Remove partitioning algorithms for sparse matrix reordering.  The
58            copyright on the Metis code was problematic and the methods were
59            rarely used.
60            * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
61            operations are now done entirely in CHOLMOD code.
62    
63    2006-09-06  Douglas Bates  <bates@R-project.org>
64    
65            * src/Mutils.h: Remove functions that are no longer used.
66    
67    2006-09-04  Douglas Bates  <bates@R-project.org>
68    
69            * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
70            * src/DEPS.mkf: update
71    
72    2006-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>
73    
74            * created branches/Matrix-for-R-2.3.x;  on trunk: do
75            * DESCRIPTION (Version): 0.9975-0
76            (Depends): R (>= 2.4.0)
77    
78    2006-09-01  Douglas Bates  <bates@R-project.org>
79    
80            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
81    
82    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
83    
84            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
85            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
86    
87            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
88    
89    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
90    
91            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
92            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
93            * R/dsparseMatrix.R: dito
94            * R/Csparse.R: dito
95    
96    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
97    
98            * R/dMatrix.R (Compare): improve availability of "<", etc
99            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
100    
101    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
102    
103            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
104            of a 0-index which was used as 1-index (..hmm)
105    
106            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
107    
108            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
109            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
110            (.is.diagonal): dito
111    
112            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
113    
114            * R/Matrix.R (Matrix): also work for NA data
115    
116    2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
117    
118            * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
119            in all cases.
120    
121    2006-08-27  Douglas Bates  <bates@R-project.org>
122    
123            * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
124            (ddense_band): Added triu, tril and band for ddenseMatrix objects.
125    
126    2006-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
127    
128            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
129            subclasses of "ddenseMatrix"
130            * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
131            * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
132            instead of half dozen specialized ones.
133    
134    2006-08-25  Douglas Bates  <bates@R-project.org>
135    
136            * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
137            <tillard@cirad.fr> - ordering standard errors to match effects.
138    
139    2006-08-24  Douglas Bates  <bates@R-project.org>
140    
141            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
142            on R_ldl.
143            * R/lCholCMatrix.R,
144            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
145            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
146            * many files in ./R and ./src: Use more general version of
147            dup_mMatrix_as_dgeMatrix to simplify method definitions.
148            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
149            dtpMatrix, dspMatrix and dppMatrix conversions.
150    
151    
152    2006-08-23  Douglas Bates  <bates@R-project.org>
153    
154            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
155            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
156            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
157            dgeMatrix_crossprod (may need to do this in other places).
158            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
159            generic and method for dsCMatrix.  Use CHOLMOD for chol().
160    
161    2006-08-22  Douglas Bates  <bates@R-project.org>
162    
163            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
164            types of classed Matrices, matrices or numeric or logical vectors.
165            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
166            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
167            to Mutils.h (as an inline) and change name to Matrix_check_class;
168            fixes in as_cholmod_factor and chm_factor_to_SEXP.
169            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
170            dsCMatrix_matrix_solve.  Comment out vestigial functions.
171            * src/Csparse.c: use diag_P and uplo_P macros.
172    
173    2006-08-21  Douglas Bates  <bates@R-project.org>
174    
175            * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
176            valgrind.
177            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
178            inverses.
179            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
180            -Wall warnings.
181            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
182            Use dup_mMatrix_as_dgeMatrix.
183    
184    2006-08-20  Douglas Bates  <bates@R-project.org>
185    
186            * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
187            * tests/sparseQR.R: Added
188            * man/sparseQR-class.Rd: Document methods for qr.* generics
189            * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
190    
191    2006-08-19  Douglas Bates  <bates@R-project.org>
192    
193            * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
194            Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
195            and qr.fitted.
196            * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
197            * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
198    
199    2006-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
200    
201            * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
202            the base version has no "..." argument.
203    
204            * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
205    
206            * R/Matrix.R: define and
207            * NAMESPACE: export as.numeric() and as.logical() methods.
208                    Let's hope these do not badly slow down something...
209            Finally export the zapsmall() method.
210    
211    2006-08-17  Douglas Bates  <bates@R-project.org>
212    
213            * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
214            R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
215            * src/dtCMatrix.c :Remove code that is no longer used
216            * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
217    
218    2006-08-14  Douglas Bates  <bates@R-project.org>
219    
220            * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
221            Csparse_to_logical and Csparse_symmetric_to_general.
222            * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
223            coercion methods between CsparseMatrix and TsparseMatrix.
224    
225    2006-08-14  Douglas Bates  <bates@R-project.org>
226    
227            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
228            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
229            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
230            possible.
231    
232    2006-08-12  Douglas Bates  <bates@R-project.org>
233    
234            * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,
235              dgTMatrix.c,dgCMatrix.c,dsCMatrix.c,dtTMatrix.c, R/dsTMatrix.R,
236              Tsparse.R,Csparse.R,dgTMatrix.R,dsCMatrix.R,lsCMatrix.R:
237              generalize conversions between TsparseMatrix, CsparseMatrix,
238              denseMatrix and matrix.  Preserve triangularity property and
239              propagate Dimnames in the easy cases.
240    
241    2006-08-10  Douglas Bates  <bates@R-project.org>
242    
243            * src/lmer.c: adjust checks in glmer_init for S4SXP
244            * tests/validObj.R: check of all(eq) should be all(eq@x) - worked
245            before S4SXP but for the wrong reasons.
246    
247    2006-08-08  Douglas Bates  <bates@R-project.org>
248    
249            * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.
250            Later modified to return the upper triangle only.
251            * R/dgTMatrix.R: Remove vestigial crossprod and tcrossprod methods.
252    
253    2006-08-07  Douglas Bates  <bates@R-project.org>
254    
255            * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
256            R-level conversion to a sparse symmetric class.
257            * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
258            Remove conversion to sparse symmetric classes (now done in C code).
259    
260    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
261    
262            * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
263            * man/band.Rd:  adapt the \dontshow{} unit test.
264    
265    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
266    
267            * DESCRIPTION (Version): 0.995-14  for CRAN
268    
269            * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
270    
271            * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
272            * tests/other-pkgs.R:  more checks, sparseMatrix -> graph
273    
274            * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
275            * R/Tsparse.R (tril, triu, band): methods
276            * R/dgRMatrix.R (tril, ...):    ditto
277            * man/band.Rd:                  ditto
278    
279    2006-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
280    
281            * R/Matrix.R (head, tail): directly use utils:::head.matrix
282                    to be up-to-date automatically.
283    
284    2006-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
285    
286            * DESCRIPTION (Version): 0.995-13 to be released to CRAN
287    
288            * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
289            * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
290            * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
291            such that the S4 objects are always created by the current version
292            of R and 'Matrix' class definitions.
293    
294    2006-08-01  Douglas Bates  <bates@R-project.org>
295    
296            * R/lmer.R (LMEoptimize method), tests/lmer.R,
297            inst/external/test3comp.rda: Added warnings for convergence on
298            boundary and test cases.
299    
300            * src/lmer.c (mer_postVar): Modified to return the variances that
301            are marginal to the fixed effects, not conditional on them (which
302            is what the bVar slot contents represent).
303    
304    2006-07-31  Douglas Bates  <bates@R-project.org>
305    
306            * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace):  Add the hatTrace
307            function which calls the C function mer_hat_trace2.
308    
309            * man/ranef.Rd: Include description of "postVar" argument and
310            producing a caterpillar plot.
311    
312    2006-07-31  Martin Maechler  <maechler@stat.math.ethz.ch>
313    
314            * NAMESPACE:    change  "correlation" to "corMatrix"
315            * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
316            * R/dpoMatrix.R: ditto
317            * R/lmer.R:      ditto
318    
319    2006-07-28  Douglas Bates  <bates@R-project.org>
320    
321            * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
322            RZXinv slot's contents into a separate internal function that can
323            be used in mer_hat_trace.
324    
325    2006-07-22  Martin Maechler  <maechler@stat.math.ethz.ch>
326    
327            * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
328            via new smart
329            * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
330            utility functions.
331    
332    
333    2006-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
334    
335            * R/Csparse.R (tril, triu, band): do return *triangular* classed
336            matrices when appropriate; band() even symmetric ones.
337            (replCmat): extend to potentially all "CsparseMatrix"
338            * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
339            allow subassignment for special sparse matrices.
340    
341            * R/Auxiliaries.R (as_geClass): factor out the  .M.kind() functionality
342    
343            * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
344            argument; in glmer_*(): print only if(verbose).
345    
346            speed-optimize a few places by moving REAL(.) out of loops.
347    
348            * src/lmer.h, src/init.h, R/lmer.R:  related to above.
349    
350    2006-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
351    
352            * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
353                    since that wrongly triggers also for M[ logi , ]
354    
355            * R/denseMatrix.R: "[" methods now also work e.g. when indexing
356            a symmetric matrix that results in a non-symmetric one.
357            * R/Auxiliaries.R (as_geClass): new function used in "[" above.
358    
359            * R/dMatrix.R: make round(M) work as round(M, 0)
360    
361            * R/dgTMatrix.R (image): coordinate system and axis now use
362            1-based indices, not 0-based ones.
363    
364            * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
365            * tests/indexing.R: test it.
366    
367            * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
368            * man/isSymmetric-methods.Rd: and document it.
369    
370            * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
371            * man/SparseM-conv.Rd: docu them
372    
373            * tests/other-pkgs.R: renamed from tests/graph.R and add example
374                    for 'SparseM' conversions
375    
376    2006-07-17  Douglas Bates  <Douglas.Bates@R-project.org>
377    
378            * R/Matrix.R (head): added head() and tail() methods.
379    
380    2006-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
381    
382            * DESCRIPTION (Version): 0.995-12 released to CRAN
383    
384    2006-07-15  Martin Maechler  <maechler@stat.math.ethz.ch>
385    
386            * tests/simple.R: add check for correct dsT -> dgT coercion;
387                    add check for correct printing of symmetric sparse matrices.
388    
389            * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
390            for sparse symmetric matrices.
391    
392            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
393            diagonal twice.
394    
395    2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>
396    
397            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
398            being applied to the x slot (detected by Brian Ripley).
399    
400    2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
401    
402            * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
403    
404            * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
405    
406    2006-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
407    
408            * src/lgCMatrix.c (lgCMatrix_diag): new function
409            * R/lgCMatrix.R (diag): for new method
410    
411            * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
412                 ==> construction of illegal "*gTMatrix" via new() should
413                 now be much less easy:
414            * tests/Class+Meth.R: assertError() for some illegal "dgT*"
415    
416            * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
417                    directly.
418            * man/Matrix.Rd: documents it.
419    
420  2006-07-06  Douglas Bates  <bates@R-project.org>  2006-07-06  Douglas Bates  <bates@R-project.org>
421    
422          * src/pedigree.c (pedigree_inbreeding): Correction in          * src/pedigree.c (pedigree_inbreeding): Correction in
# Line 9  Line 428 
428          objects.  Modified validity check on pedigree objects to account          objects.  Modified validity check on pedigree objects to account
429          for nonparallel patterns of missingness of parents.          for nonparallel patterns of missingness of parents.
430    
431            * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
432            class.
433    
434    2006-07-01  Martin Maechler  <maechler@stat.math.ethz.ch>
435    
436            * R/pMatrix.R: coercion pMatrix -> Tsparse
437    
438  2006-06-12  Douglas Bates  <bates@R-project.org>  2006-06-12  Douglas Bates  <bates@R-project.org>
439    
440            * DESCRIPTION (Version): 0.995-11 released to CRAN
441    
442          * R/lmer.R (mcmcsamp method): Corrected arrangments of names on          * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
443          the output from mcmcsamp.          the output from mcmcsamp.
444    
# Line 23  Line 451 
451    
452          * R/diagMatrix.R (setAs): define coercion methods to sparse matrix          * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
453          classes.          classes.
454            * R/sparseMatrix.R etc: multiplication of diagonal and sparse
455    
456  2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
457    
# Line 60  Line 489 
489    
490          * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use          * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
491          the C code depending on a slot structure that's no longer valid.          the C code depending on a slot structure that's no longer valid.
492          * src/dgTMatrix.c: dito (also: src/init.c src/dgTMatrix.h)          * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
493    
494    
495  2006-05-17  Douglas Bates  <bates@stat.wisc.edu>  2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
# Line 183  Line 612 
612          * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)          * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
613          * man/KNex.Rd: and other help files          * man/KNex.Rd: and other help files
614          * tests/*.R: several ones needed adaption          * tests/*.R: several ones needed adaption
615          * inst/doc/Comparisons.Rnw: dito          * inst/doc/Comparisons.Rnw: ditto
616    
617  2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
618    
# Line 387  Line 816 
816  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
817    
818          * R/Matrix.R:  added first "[<-" methods; not yet functional          * R/Matrix.R:  added first "[<-" methods; not yet functional
819          * R/denseMatrix.R: dito          * R/denseMatrix.R: ditto
820          * man/Subassign-methods.Rd: new help file for these          * man/Subassign-methods.Rd: new help file for these
821    
822  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>

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