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revision 1716, Sat Jan 6 02:01:24 2007 UTC revision 1961, Fri Jul 6 21:33:47 2007 UTC
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1    2007-07-06  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * DESCRIPTION (Version): 0.999375 merged into the trunk; ready for
4            release.
5    
6    2007-07-06 14:11  Douglas Bates <bates@stat.wisc.edu>
7    
8            * [r4559] src/iohb.c, src/iohb.h: Remove Harwell-Boeing input/output
9              functions - no longer used
10            * [r4560] src/HBMM.c, src/Mutils.c, src/dgTMatrix.c, src/dgeMatrix.c,
11              src/dspMatrix.c, src/dsyMatrix.c, src/dtCMatrix.c,
12              src/factorizations.c, src/sparseQR.c: Replace most calls to Calloc by
13              Alloca
14    
15    2007-07-06 13:14  Martin Maechler <maechler@stat.math.ethz.ch>
16    
17            * [r4558] inst/doc/Comparisons.Rnw, src/CHMfactor.c, src/Csparse.c,
18              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dense.c,
19              src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c, src/sparseQR.c,
20              src/t_gCMatrix_colSums.c: more R_CheckStack()s
21    
22    2007-07-05 18:12  Douglas Bates <bates@stat.wisc.edu>
23    
24            * [r4550] inst/include/Matrix.h: Add the macro N_AS_CHM_DN to "alloca"
25              the required amount of memory then call M_numeric_as_chm_dense.
26            * [r4556] src/Mutils.h, src/dgCMatrix.c: Define and use the Alloca macro
27              (like Calloc but calling alloca)
28    
29    2007-07-05  Martin Maechler  <maechler@stat.math.ethz.ch>
30    
31            * R/sparseMatrix.R (printSpMatrix): renamed from prSpMatrix()
32            and extended with more sophisticated 'col.names' option.
33            * NAMESPACE: export  printSparseMatrix()
34            * man/printSpMatrix.Rd: document, incl. examples
35    
36    2007-07-04 16:21  Douglas Bates <bates@stat.wisc.edu>
37    
38            * [r4543] src/cs_utils.c, src/cs_utils.h, src/dgCMatrix.c,
39              src/dtCMatrix.c, src/sparseQR.c: CSP typedef for *cs and macro
40              AS_CSP. API change - pass the empty structure to Matrix_as_cs.
41    
42    2007-07-04  Martin Maechler  <maechler@stat.math.ethz.ch>
43    
44            * DESCRIPTION (Version): 0.99875-4
45    
46            * tests/Class+Meth.R (tstMatrixClass): add dimnames, and hence test
47            some dimnames perservation.
48    
49            * R/dsTMatrix.R (t-method): keep dimnames
50            * R/dtTMatrix.R:  ditto
51    
52            * R/sparseMatrix.R (prSpMatrix): print colnames when non-trivial
53            and ncol(.) < 10
54    
55            * src/cs_utils.c: drop check_class() and use Matrix_check_class()
56            from Mutils.h
57    
58            * src/lgCMatrix.c ([ln]csc_to_matrix): no longer lose dimnames,
59            e.g. in as(<ngCMatrix>, "matrix")
60    
61    2007-07-01 13:27  Douglas Bates <bates@stat.wisc.edu>
62    
63            * [r4529] .: Create a branch for the API changes from the 0.99875
64              series to the 0.999375 series
65            * [r4530] DESCRIPTION, inst/include/Matrix.h,
66              inst/include/Matrix_stubs.c, src/CHMfactor.c, src/Csparse.c,
67              src/Mutils.h, src/Tsparse.c, src/chm_common.c, src/chm_common.h,
68              src/dense.c, src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c,
69              src/t_gCMatrix_colSums.c: API change - pass the empty structure to the
70              as_cholmod_x functions
71    
72    2007-06-30 09:05  Martin Maechler <maechler@stat.math.ethz.ch>
73    
74            * [r4527] trunk/Matrix/DESCRIPTION, trunk/Matrix/NAMESPACE,
75              trunk/Matrix/inst/doc/Comparisons.Rnw: add session- and hardware-info
76              to Comparisons
77    
78    >>>>>>> .merge-right.r4561
79    2007-06-29  Martin Maechler  <maechler@stat.math.ethz.ch>
80    
81            * DESCRIPTION (Version): 0.99875-3 ready to be released.
82    
83            * R/sparseMatrix.R (spMatrix): make spMatrix(3,4) working
84    
85            * R/AllGeneric.R: set "Math" (and "Math2") group generics in a way
86            that should also work in a future version of R.
87    
88    2007-06-21  Martin Maechler  <maechler@stat.math.ethz.ch>
89    
90            * NAMESPACE, R/AllClass.R: "xsparseVector" class union.
91    
92            * R/sparseVector.R: more *sparseVector coercions, notably for
93            non - double ones.
94    
95    2007-06-19  Martin Maechler  <maechler@stat.math.ethz.ch>
96    
97            * R/colSums.R: new file for all (col|row)(Sums|Means) methods,
98              notably the new ones building on the new .Call(.)s:
99    
100            * src/dgCMatrix.c (DEF_gCMatrix_COLSUMS): use to define
101            all 4 of [dlin]gCMatrix_colSums().
102    
103    2007-06-18 16:12  Douglas Bates <bates@stat.wisc.edu>
104    
105            * [r4472] src/Syms.h, src/init.c: Added Matrix_lengthSym
106            * [r4473] src/dgCMatrix.c: Modified dgCMatrix_colSums for sparseVector
107              result
108    
109    2007-06-16  Martin Maechler  <maechler@stat.math.ethz.ch>
110    
111            * R/kronecker.R: fix typo (could lead to inf.recursion)
112            * test/simple.R: testing that
113    
114            * R/sparseMatrix.R (prSpMatrix): change to be used as print()
115            method as well (which can have arguments, show() can't).
116    
117    2007-06-16 15:52  Douglas Bates <bates@stat.wisc.edu>
118    
119            * [r4466] R/dgCMatrix.R, src/dgCMatrix.c, src/dgCMatrix.h, src/init.c:
120              added dgCMatrix_colSums for [col,row][Sums,Means]
121    
122    2007-06-15 23:15  Douglas Bates <bates@stat.wisc.edu>
123    
124            * [r4460] R/sparseMatrix.R, man/dgCMatrix-class.Rd, src/dgCMatrix.c,
125              src/dgCMatrix.h, src/init.c: added lm.fit.sparse (unexported),
126              coercion of "factor" to "dgCMatrix" and dgCMatrix_cholsol
127            * [r4461] R/AllClass.R, man/sparseMatrix-class.Rd: draft "indicators"
128              class
129            * [r4463] R/sparseMatrix.R, man/dgCMatrix-class.Rd,
130              man/sparseMatrix-class.Rd: Don't need an "indicators" class - use the
131              row names to store the levels - duh!  Added an example.
132    
133    2007-06-14  Martin Maechler  <maechler@stat.math.ethz.ch>
134    
135            * src/Csparse.c (Csparse_validate): check for *repeated* entries
136            thanks to example from Christian Buchta; with a test here:
137            * tests/simple.R:
138    
139    2007-06-07  Martin Maechler  <maechler@stat.math.ethz.ch>
140    
141            * R/Auxiliaries.R (callGeneric): another fix, needed for some cases
142            of colSums(*, sparseResult = TRUE)
143    
144    2007-06-06  Martin Maechler  <maechler@stat.math.ethz.ch>
145    
146            * R/lsparseMatrix.R, R/ldenseMatrix.R (all, any): change default to
147            'na.rm = FALSE' as "everywhere" else in R.
148    
149    2007-06-05 Douglas Bates <bates@stat.wisc.edu>
150    
151            * [r4421] src/CSparse_install.sh: Modify for new organization of
152              CSparse package
153            * [r4425] src/UFsparse_download.sh: Update to version 3.0.0 of
154              SuiteSparse
155            * [r4426] src/Makefile: add ./UFconfig to the include path for
156              compilation
157            * [r4427] src/cs.[ch]: update to CSparse version 2.2.0
158            * [r4428] inst/doc/UFsparse/* src/{AMD,CHOLMOD,COLAMD}/*
159              src/UFconfig/UFconfig.h: Update to version 3.0.0 of SuiteSparse
160    
161    2007-06-05  Martin Maechler  <maechler@stat.math.ethz.ch>
162    
163            * R/Auxiliaries.R (emptyColnames): + argument msg.if.not.empty, used in
164            * R/sparseMatrix.R (prSpMatrix): now gives a message about
165            suppressed column names.
166    
167    2007-06-04 17:13  Douglas Bates <bates@stat.wisc.edu>
168    
169            * [r4418] src/Csparse.c, src/HBMM.c, src/Mutils.c, src/Mutils.h,
170              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dgCMatrix.c,
171              src/dgeMatrix.c, src/dpoMatrix.c, src/dpoMatrix.h, src/dppMatrix.c,
172              src/dppMatrix.h, src/dsCMatrix.c, src/dspMatrix.c, src/dspMatrix.h,
173              src/dsyMatrix.c, src/dsyMatrix.h, src/dtpMatrix.c, src/dtrMatrix.c:
174              Remove warnings after change to const char* CHAR
175    
176    2007-06-04 17:11  Douglas Bates <bates@stat.wisc.edu>
177    
178            * [r4417] inst/include/Matrix_stubs.c, inst/include/cholmod.h: Corrected
179              type of M_cholmod_ssmult
180    
181    2007-06-03 14:42  Douglas Bates <bates@stat.wisc.edu>
182    
183            * [r4412] inst/include/Matrix_stubs.c, inst/include/cholmod.h,
184              src/init.c: Yet another cholmod export - cholmod_ssmult
185    
186    2007-05-23  Martin Maechler  <maechler@stat.math.ethz.ch>
187    
188            * NAMESPACE: exported drop0(), since
189            * man/drop0.Rd: I have seen several cases, I really wanted to use
190            it, so our users may want too.
191    
192    2007-05-22  Martin Maechler  <maechler@stat.math.ethz.ch>
193    
194            * man/colSums.Rd: separately document colSums() etc, since these
195            have the extra argument 'sparseResult'.
196    
197    2007-05-21  Martin Maechler  <maechler@stat.math.ethz.ch>
198    
199            * R/sparseMatrix.R (spMatrix): utility (T)sparse Matrix constructor;
200            * man/spMatrix.Rd: docu., including examples
201    
202            * R/Auxiliaries.R (sp.colMeans): etc, using a patched callGeneric(),
203            in order to make colMeans() etc fast *and* correct.
204            * R/sparseVector.R (replSPvec): "[<-" functionality for
205            sparseVectors; tested in
206            * tests/simple.R:
207    
208    2007-05-19  Martin Maechler  <maechler@stat.math.ethz.ch>
209    
210            * R/sparseMatrix.R (print.sparseSummary): and summary() method for
211            (very) sparse Matrices; output similar to Matlab's print().
212    
213    2007-05-17  Douglas Bates  <bates@stat.wisc.edu>
214    
215            * src/HBMM.c (Matrix_writeMatrixMarket): Write 1-based, not
216            0-based, indices (Jose Quesada <quesada@gmail.com>).
217    
218    2007-05-16  Douglas Bates  <bates@stat.wisc.edu>
219    
220            * R/CHMfactor.R: Added solve methods for a CHMfactor object.
221    
222    2007-05-16  Martin Maechler  <maechler@stat.math.ethz.ch>
223    
224            * R/Auxiliaries.R (sparsapply): new utility, much faster than
225            tapply1() for large sparse matrices.
226    
227    2007-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
228    
229            * R/Matrix.R (dim<-): reshape now via sparseVector.
230    
231            * R/sparseVector.R: methods and function for
232            * R/AllClass.R: new "sparseVector" class and daughters.
233            * NAMESPACE: export new classes
234    
235    2007-05-14  Martin Maechler  <maechler@stat.math.ethz.ch>
236    
237            * DESCRIPTION (Version): 0.99875-1
238            * src/Makefile.win: also remove Lapack code from here (cf. 04-25).
239    
240    2007-05-11  Martin Maechler  <maechler@stat.math.ethz.ch>
241    
242            * R/Tsparse.R ([, Tsparse): fix last case: *duplicated*, symmetric
243            indexing
244            * tests/indexing.R: test set for that.
245    
246    2007-05-08  Martin Maechler  <maechler@stat.math.ethz.ch>
247    
248            * R/Tsparse.R (replTmat): fix the case of *duplicated* index
249            entries.
250            * tests/indexing.R(out): add regression test for it
251    
252    2007-04-30  Martin Maechler  <maechler@stat.math.ethz.ch>
253    
254            * R/(l(dense|sparse))?Matrix.R (!): use 'x', not 'e1' as argument
255            name for "!" method definitions.
256    
257    2007-04-26  Martin Maechler  <maechler@stat.math.ethz.ch>
258    
259            * R/Tsparse.R (intI): new utility, used for "[" :
260                    Cleanup up there, and fixes for duplicated indices - more TODO!
261    
262            * tests/indexing.R(out): more tests
263    
264    2007-04-25  Douglas Bates  <bates@stat.wisc.edu>
265    
266            * DESCRIPTION,src/Makefile: require R>= 2.5.0 and remove Lapack
267            code that is now part of the R Lapack library.
268    
269            * src/init.c,inst/include/{Matrix_stubs.c,cholmod.h}:export
270            cholmod_factorize_p (used in lme4 for GLMMs and NLMMs).
271    
272    2007-04-21  Martin Maechler  <maechler@stat.math.ethz.ch>
273    
274            * R/Matrix.R (image): method for all Matrices, not just sparse ones.
275    
276    2007-04-17  Martin Maechler  <maechler@stat.math.ethz.ch>
277    
278            * R/Auxiliaries.R (tapply1): unname(.) -> colSums() etc don't end
279            up with extraneous names '0'...'<n-1>'
280    
281    2007-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
282    
283            * R/dgTMatrix.R (mat2dgT): care about NAs
284    
285    2007-04-11  Martin Maechler  <maechler@stat.math.ethz.ch>
286    
287            * R/kronecker.R: triangularity preserving methods
288    
289    2007-03-27  Martin Maechler  <maechler@stat.math.ethz.ch>
290    
291            * R/kronecker.R: new file collecting kronecker() methods in one
292                    place.  Goal: become much faster!
293    
294    2007-03-23  Martin Maechler  <maechler@stat.math.ethz.ch>
295    
296            * src/dtCMatrix.c (dtCMatrix_solve): use the new code from Kasper
297            Kristensen based cs_spsolve() instead of _lsolve & _usolve which
298            can be much faster.
299    
300            * tests/matprod.R: add regression tests for these (upper & lower).
301    
302    2007-03-19  Martin Maechler  <maechler@stat.math.ethz.ch>
303    
304            * R/Matrix.R (diff): method for our Matrices.
305    
306            * R/sparseMatrix.R (isDiagonal): check dim()!
307    
308    2007-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
309    
310            * R/Matrix.R (dim<-): new method for "reshape()" built on a
311            proposal from Tamas Papp.
312    
313    2007-03-16  Martin Maechler  <maechler@stat.math.ethz.ch>
314    
315            * R/AllGeneric.R: remove all  if(!isGeneric(.))  clauses
316    
317            * R/zzz.R (.onLoad, .onUnload): do *not* leave bind_activation(TRUE);
318            rather define and export  cBind() and rBind() only.
319            --> useRs *must* change code that used to have cbind()/rbind() !!
320    
321            * R/bind.R: change tests from cbind() to cBind() and similarly to rBind()
322            * R/bind.Rout.save: ditto
323    
324    2007-02-16  Douglas Bates  <bates@r-project.org>
325    
326            * DESCRIPTION (Date, Version): 0.9975-11 with new date
327            * src/dgCMatrix.c (R_to_CMatrix, compressed_to_TMatrix): remove
328            const modifier on declaration of the array 'valid'
329    
330    2007-02-12  Douglas Bates  <bates@stat.wisc.edu>
331    
332            * R/CHMfactor.R: Add image method (coercion to sparseMatrix).
333    
334    2007-02-05  Martin Maechler  <maechler@stat.math.ethz.ch>
335    
336            * DESCRIPTION (Date, Version): 0.9975-10 with new date.
337    
338            * R/Ops.R (Arith): make sure Csparse o Csparse also works for e.g. ntCMatrix
339            * tests/simple.R: test the above and some of these coercions:
340    
341            * R/nsparseMatrix.R: coercing "Csparse" to "lsparseMatrix";
342                    be careful to avoid infinite recursion, using new coercions in
343            * R/ngCMatrix.R and nsC... and ntC...
344            * R/lsparseMatrix.R: ditto
345    
346            * R/SparseM-conv.R: more conversion, notably for triplet matrices.
347    
348            * src/dgCMatrix.c (R_to_C_Matrix): port Doug's fix and
349            * R/Rsparse.R: reactivate .Call()s
350    
351            * tests/Class+Meth.R: a bit more on actual classes
352    
353    2007-02-04  Douglas Bates  <bates@stat.wisc.edu>
354    
355            * src/dgCMatrix.c (compressed_to_TMatrix): fix memory bug using strdup()
356    
357    2007-02-03  Martin Maechler  <maechler@stat.math.ethz.ch>
358    
359            * DESCRIPTION (Version): 0.9975-10 to upload
360    
361            * tests/Class+Meth.R (tstMatrixClass): require coercions to
362            specific classes less unconditionally.
363    
364            * R/Auxiliaries.R: get rid of as_Tsparse() and as_Rsparse()
365    
366            * R/Tsparse.R (triu): etc, use as(*, "TsparseMatrix") instead of as_Tsparse()
367    
368            * R/Rsparse.R (.R.2.T): R-level workaround using compressed_to_TMatrix.
369            * R/Rsparse.R (.R.2.C): R-level workaround since C-level
370            R_to_CMatrix segfaults on one platform.
371            Eliminate most coercion method to *specific* classes, and replace
372            with virtual classes coercions.
373    
374    
375    2007-02-01  Martin Maechler <maechler@stat.math.ethz.ch>
376    
377            * src/init.c: export the CHM...._validate() placeholders, since
378            they *are* called.
379    
380            * tests/Class+Meth.R (classCanCoerce): and starting to test
381            all as(<from>, <to>)
382    
383    2007-01-30  Martin Maechler  <maechler@stat.math.ethz.ch>
384    
385            * R/Tsparse.R ([): more care when subsetting triangular Tsparse
386            * tests/indexing.R: tested now
387            * tests/indexing.Rout.save: updated
388    
389            * src/Csparse.c (Csparse_to_dense): use Rkind = -1 for PATTERN to
390            * src/chm_common.c (chm_dense_to_SEXP): return "ngeMatrix" when
391            appropriate.
392    
393            * NAMESPACE: export a trivial
394            * R/Matrix.R: drop() Matrix-method
395    
396            * R/AllClass.R: moved all prototypes to virtual super classes.
397    
398            * R/Rsparse.R: many more coercions to have less exceptions in
399            * tests/Class+Meth.R:
400    
401            * R/Ops.R (Compare): tweak for case with NA
402            * tests/simpl.R: hence another 'FIXME' eliminated
403    
404    2007-01-29  Martin Maechler  <maechler@stat.math.ethz.ch>
405    
406            * R/diagMatrix.R (solve): the obvious methods for diagonalMatrix
407            objects.
408    
409            * tests/Class+Meth.R (tstMatrixClass): now testing diag(), nnzero(),
410              and more of "!", "&", "|", all, any; coercions
411    
412            * R/Rsparse.R: many coercions (which enable quite a few other
413            methods), thanks to enhancements in
414            * src/dgCMatrix.c (R_to_CMatrix): new, and
415            * src/dgCMatrix.c (compressed_to_TMatrix): now for (d,l,n) ,
416            symmetric & triangular and ..RMatrix objects.
417    
418            * src/TMatrix_as.c (Matrix_T_as_DENSE,Matrix_T_as_GENERAL):
419            renamed file from src/dsTMatrix.c;
420            now dealing with symmetric and triangular Tsparse coercions, both
421            to dense and general.
422    
423    2007-01-27  Martin Maechler  <maechler@stat.math.ethz.ch>
424    
425            * src/dsTMatrix.c: has now "l" and "n" methods besides the "d" ones.
426    
427            * R/Ops.R (Arith): <dgCMatrix> o <numeric> now remains sparse
428            where sensible when the <numeric> is of length > 1.
429    
430    2007-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
431    
432            * R/Matrix.R ([<-): for M[] <- value: fix length
433    
434    2007-01-25  Martin Maechler  <maechler@stat.math.ethz.ch>
435    
436            * R/Auxiliaries.R (n2l_Matrix): new, to be used in
437            * R/ndenseMatrix.R: new coercions n* -> l*
438    
439    2007-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
440    
441            * R/triangularMatrix.R: new file; simple triu() and tril() methods.
442    
443            * R/Ops.R ("Logic"): and other "Ops", many updates
444    
445    2007-01-18  Martin Maechler  <maechler@stat.math.ethz.ch>
446    
447            * src/Mutils.h (SET_DimNames): new utility
448    
449            * R/Auxiliaries.R (nnzero): improved and now exported via
450    
451            * NAMESPACE: + nnzero(); length() == prod(dim(.)) method for all "Matrix" objects
452    
453    2007-01-17  Martin Maechler  <maechler@stat.math.ethz.ch>
454    
455            * R/diagMatrix.R (!): fix typo.
456    
457    2007-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
458    
459            * R/Auxiliaries.R (as_Csparse): and quite a few others:
460                    allow to pass class definition --> speedup
461            * R/sparseMatrix.R: apply the above
462    
463            * R/Csparse.R: coercion Csparse* to dense* now preserves shape properties.
464    
465            * src/Mutils.h (mMatrix_as_geMatrix): new, based on
466            * src/Mutils.c (dup_mMatrix_as_geMatrix): new; generalization of
467            old dup_mMatrix_as_dgeMatrix), eliminating a long-standing "FIXME".
468    
469            * src/dense.c (dense_to_Csparse): use new mMatrix_as_geMatrix()
470    
471            * R/denseMatrix.R (.dense2C): based on dense_to_Csparse: name it,
472            and use it for "sparse*" as well, since it's faster than the
473            as_Csparse(.) way.
474    
475    2007-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
476    
477            * R/Ops.R ("Logic"): more methods, notably an  <lgC> o <lgC> one.
478    
479    2007-01-12  Martin Maechler  <maechler@stat.math.ethz.ch>
480    
481            * R/Tsparse.R (.TM.repl.i.2col): new internal function to be used
482            as method for   M[ ij ] <- v
483            * R/Csparse.R:: go via Tsparse for "M[ij] <- v"
484    
485            * R/Ops.R: "Compare" for (C|R)sparse: need pointer slot for all
486            FALSE answer
487    
488            * R/Csparse.R (replCmat): fix the "all non-zero" case with reordering
489            * tests/indexing.R: test it, and some of the above
490    
491    2007-01-05  Martin Maechler  <maechler@stat.math.ethz.ch>
492    
493            * R/Auxiliaries.R (is_duplicatedT): new utility
494    
495  2007-01-05  Douglas Bates  <bates@stat.wisc.edu>  2007-01-05  Douglas Bates  <bates@stat.wisc.edu>
496    
497          * src/init.c (R_init_Matrix): export cholmod_scale          * src/init.c (R_init_Matrix): export cholmod_scale
498    
499    2006-12-30  Martin Maechler  <maechler@stat.math.ethz.ch>
500    
501            * R/zzz.R (tmp): for R >= 2.5.0, extend formals of our
502            base::as.matrix to (x, ...)
503    
504  2006-12-28  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-12-28  Martin Maechler  <maechler@stat.math.ethz.ch>
505    
506          * 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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