R gurus:
I'm trying to get another round of rconifers out and I need some advice/help
crushing differences in the examples test.
I'm trying to make sure the max sdi values are being respected.
I've added a tests/rconifers-Ex.Rout.save (from windows i386-pc-mingw32) and
when I ran R CMD check (both R-2.13.0), I got the following results:
* using log directory 'c:/conifers/trunk/rconifers.Rcheck'
* using R version 2.13.0 (2011-04-13)
* using platform: i386-pc-mingw32 (32-bit)
* using session charset: ISO8859-1
* checking for file 'rconifers/DESCRIPTION' ... OK
* this is package 'rconifers' version '1.0.7'
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking for executable files ... OK
* checking whether package 'rconifers' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... WARNING
Found the following sources/headers with CR or CRLF line endings:
src/coeffs_cips.c
src/coeffs_mgt.c
src/coeffs_smc.c
src/coeffs_swo.c
src/coeffs_swohybrid.c
src/conifers.h
src/file_io.c
src/grow.c
src/model_cips.c
src/model_smc.c
src/model_swo.c
src/model_swohybrid.c
src/mortality.c
src/plot.c
src/rconifers.c
src/stats.c
src/thin.c
Some Unix compilers require LF line endings.
* checking line endings in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking examples ... OK
* checking differences from 'rconifers-Ex.Rout' to 'rconifers-Ex.Rout.save' ...
OK
* checking PDF version of manual ... OK
WARNING: There was 1 warning, see
'c:/conifers/trunk/rconifers.Rcheck/00check.log'
for details
The magic line is:
* checking differences from 'rconifers-Ex.Rout' to 'rconifers-Ex.Rout.save' ...
OK
which tells me that the check file matched the expected file.
When I ran the check under OSX and got the following results:
macbook:Desktop hamannjd$ R CMD check rconifers
* using log directory ‘/Users/hamannjd/Desktop/rconifers.Rcheck’
* using R version 2.13.0 (2011-04-13)
* using platform: x86_64-apple-darwin10.7.0 (64-bit)
* using session charset: UTF-8
* checking for file ‘rconifers/DESCRIPTION’ ... OK
* this is package ‘rconifers’ version ‘1.0.7’
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking for executable files ... OK
* checking whether package ‘rconifers’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking examples ... OK
* checking differences from ‘rconifers-Ex.Rout’ to ‘rconifers-Ex.Rout.save’ ...
0a1
options(pager = "console")
377,383c378,384
< 1 1 DF 2.08 0.61 7.08 0.845 1 100 4.40 0
< 2 1 PP 4.80 2.91 11.50 0.852 1 100 7.55 0
< 3 2 IC 0.60 0.00 1.70 0.706 1 100 1.17 0
< 4 2 PP 0.51 0.00 1.34 0.478 1 100 1.37 0
< 5 2 IC 0.50 0.00 1.06 0.623 1 100 0.98 0
< 6 2 IC 0.34 0.00 0.76 0.474 1 100 0.60 0
< 7 2 IC 0.17 0.00 0.58 0.310 1 100 0.29 0
---
1 1 DF 2.08 0.61 7.08 0.845 1 100.00 4.400000 0
2 1 PP 4.80 2.91 11.50 0.852 1 100.00 7.550000 0
3 2 WF 49.00 35.20 77.96 0.368 1 2.96 30.152669 0
4 2 PP 2.43 1.10 6.28 0.705 1 100.00 3.773147 0
5 2 COCO 0.49 0.00 3.90 1.000 18 100.00 2.360064 0
6 2 DF 1.06 0.00 3.88 0.794 1 100.00 2.973220 0
7 2 IC 0.60 0.00 1.70 0.706 1 100.00 1.170000 0
2076c2077
< max sdi = 400.955
---
max sdi = 400.222
2078,2084c2079,2085
< CEIN 0.000000 8.57557 0.000000 250.00 250.00
< COCO 0.000000 10.65750 0.000000 825.00 825.00
< DF 3.871848 32.37521 34.749737 425.00 425.00
< IC 0.680329 7.94603 0.757329 300.00 500.00
< PM 4.882285 33.89248 84.505614 650.00 650.00
< PP 10.747477 42.37973 62.999774 100.00 100.00
< WF 1.961988 7.49918 5.264321 250.74 275.74
---
CEIN 0.000000 8.83025 0.00000 250.00 250.00
COCO 0.000000 10.52370 0.00000 825.00 825.00
DF 3.380206 28.96161 26.48507 425.00 425.00
IC 0.997025 8.10528 1.49098 275.00 500.00
PM 5.036259 34.20425 89.91983 650.00 650.00
PP 10.505312 41.18743 60.19271 100.00 100.00
WF 2.089732 7.81061 5.37670 225.74 275.74
2094c2095
< max sdi = 400.955
---
max sdi = 400.222
2096,2102c2097,2103
< CEIN 0.000000 8.57557 0.000000 250.00 250.00
< COCO 0.000000 10.65750 0.000000 825.00 825.00
< DF 3.871848 32.37521 34.749737 425.00 425.00
< IC 0.680329 7.94603 0.757329 300.00 500.00
< PM 4.882285 33.89248 84.505614 650.00 650.00
< PP 10.747477 42.37973 62.999774 100.00 100.00
< WF 1.961988 7.49918 5.264321 250.74 275.74
---
CEIN 0.000000 8.83025 0.00000 250.00 250.00
COCO 0.000000 10.52370 0.00000 825.00 825.00
DF 3.380206 28.96161 26.48507 425.00 425.00
IC 0.997025 8.10528 1.49098 275.00 500.00
PM 5.036259 34.20425 89.91983 650.00 650.00
PP 10.505312 41.18743 60.19271 100.00 100.00
WF 2.089732 7.81061 5.37670 225.74 275.74
2513c2514
< max sdi = 398.99
---
max sdi = 398.321
2515,2521c2516,2522
< CEIN 0.00000 8.74666 0.000000 250.00 250.00
< COCO 0.00000 10.60946 0.000000 825.00 825.00
< DF 3.17032 28.17772 23.298195 425.00 425.00
< IC 1.02363 6.08777 0.857239 150.00 500.00
< PM 5.02216 33.93141 89.417000 650.00 650.00
< PP 10.53209 40.19664 60.500008 100.00 100.00
< WF 2.52830 5.38780 5.255483 150.74 275.74
---
CEIN 0.00000 8.73566 0.000000 250.00 250.00
COCO 0.00000 10.60959 0.000000 825.00 825.00
DF 3.11552 27.87012 22.499678 425.00 425.00
IC 1.02147 6.04613 0.853626 150.00 500.00
PM 5.01949 33.92538 89.322114 650.00 650.00
PP 10.60861 40.42145 61.382237 100.00 100.00
WF 2.52834 5.37677 5.255645 150.74 275.74
2535c2536
< max sdi = 392.682
---
max sdi = 392.183
2537,2543c2538,2544
< CEIN 0.00000 8.74666 0.000000 250.0000 250.0000
< COCO 0.00000 10.60946 0.000000 825.0000 825.0000
< DF 6.12078 42.83671 10.413135 50.9615 50.9615
< IC 1.02363 6.08777 0.857239 150.0000 500.0000
< PM 5.02216 33.93141 89.417000 650.0000 650.0000
< PP 10.53209 40.19664 60.500008 100.0000 100.0000
< WF 2.52830 5.38780 5.255483 150.7400 275.7400
---
CEIN 0.00000 8.73566 0.000000 250.0000 250.0000
COCO 0.00000 10.60959 0.000000 825.0000 825.0000
DF 6.01295 42.00488 10.049466 50.9615 50.9615
IC 1.02147 6.04613 0.853626 150.0000 500.0000
PM 5.01949 33.92538 89.322114 650.0000 650.0000
PP 10.60861 40.42145 61.382237 100.0000 100.0000
WF 2.52834 5.37677 5.255645 150.7400 275.7400
2555c2556
< max sdi = 390.319
---
max sdi = 389.507
2557,2563c2558,2564
< CEIN 0.00000 8.74666 0.0000000 250.00000 250.00000
< COCO 0.00000 10.60946 0.0000000 825.00000 825.00000
< DF 6.25984 44.26174 3.2535039 15.22296 15.22296
< IC 1.20533 11.86522 0.0609674 7.69418 11.76394
< PM 4.85482 33.74425 2.0646472 16.06105 16.06105
< PP 11.23175 42.87801 8.8974623 12.93139 12.93139
< WF 3.77143 6.55036 0.3592728 4.63112 6.08461
---
CEIN 0.00000 8.73566 0.0000000 250.00000 250.00000
COCO 0.00000 10.60959 0.0000000 825.00000 825.00000
DF 6.15956 43.58377 3.1501027 15.22296 15.22296
IC 1.20280 11.77230 0.0607118 7.69418 11.76394
PM 4.84104 33.71376 2.0529479 16.06105 16.06105
PP 11.34546 43.47322 9.0785299 12.93139 12.93139
WF 3.77112 6.46029 0.3592136 4.63112 6.08461
2575c2576
< max sdi = 380.439
---
max sdi = 380.211
2577,2578c2578,2579
< CEIN 0.00000 8.74666 0.00000 250.00 250.00
< COCO 0.00000 10.60946 0.00000 825.00 825.00
---
CEIN 0.00000 8.73566 0.00000 250.00 250.00
COCO 0.00000 10.60959 0.00000 825.00 825.00
2581,2583c2582,2584
< PM 5.44998 35.20515 12.15001 75.00 75.00
< PP 11.68521 44.09759 28.47847 38.24 38.24
< WF 35.20006 78.07609 5.00086 0.74 0.74
---
PM 5.45033 35.20515 12.15159 75.00 75.00
PP 11.79190 44.68573 29.00089 38.24 38.24
WF 35.20006 78.07794 5.00086 0.74 0.74
2595c2596
< max sdi = 392.617
---
max sdi = 391.885
2597,2603c2598,2604
< CEIN 0.00000 8.74666 0.000000 250.00 250.00
< COCO 0.00000 10.60946 0.000000 825.00 825.00
< DF 3.17032 28.17772 23.298195 425.00 425.00
< IC 1.02363 6.08777 0.857239 150.00 500.00
< PM 5.21231 34.66273 16.670145 112.50 112.50
< PP 10.53209 40.19664 60.500008 100.00 100.00
< WF 2.52830 5.38780 5.255483 150.74 275.74
---
CEIN 0.00000 8.73566 0.000000 250.00 250.00
COCO 0.00000 10.60959 0.000000 825.00 825.00
DF 3.11552 27.87012 22.499678 425.00 425.00
IC 1.02147 6.04613 0.853626 150.00 500.00
PM 5.20525 34.64531 16.624992 112.50 112.50
PP 10.60861 40.42145 61.382237 100.00 100.00
WF 2.52834 5.37677 5.255645 150.74 275.74
3543,3544c3544,3545
< x0 = 6.83298
< max sdi = 398.507
---
x0 = 6.83124
max sdi = 398.773
3546,3552c3547,3553
< CEIN 0.00000 8.76683 0.000000 250.0000 250.0000
< COCO 0.00000 10.60933 0.000000 825.0000 825.0000
< DF 3.14048 27.68502 21.449519 398.7488 398.7488
< IC 1.01997 6.15100 0.798552 140.7349 469.1162
< PM 5.02023 33.92625 83.829537 609.8511 609.8511
< PP 10.60746 40.60003 57.578321 93.8232 93.8232
< WF 2.53410 5.48953 4.953497 141.4292 258.7082
---
CEIN 0.00000 8.74366 0.00000 250.0000 250.0000
COCO 0.00000 10.61129 0.00000 825.0000 825.0000
DF 3.16517 28.02873 21.78805 398.7488 398.7488
IC 1.00100 6.04754 0.76913 140.7349 469.1162
PM 5.01960 33.92487 83.80863 609.8511 609.8511
PP 10.57284 40.39489 57.20315 93.8232 93.8232
WF 2.53248 5.45694 4.94718 141.4292 258.7082
3565,3566c3566,3567
< x0 = 6.83298
< max sdi = 392.685
---
x0 = 6.83124
max sdi = 392.866
3568,3574c3569,3575
< CEIN 0.00000 8.76683 0.000000 250.0000 250.0000
< COCO 0.00000 10.60933 0.000000 825.0000 825.0000
< DF 6.06366 42.37577 10.219698 50.9615 50.9615
< IC 1.01997 6.15100 0.798552 140.7349 469.1162
< PM 5.02023 33.92625 83.829537 609.8511 609.8511
< PP 10.60746 40.60003 57.578321 93.8232 93.8232
< WF 2.53410 5.48953 4.953497 141.4292 258.7082
---
CEIN 0.00000 8.74366 0.00000 250.0000 250.0000
COCO 0.00000 10.61129 0.00000 825.0000 825.0000
DF 6.10480 42.74745 10.35884 50.9615 50.9615
IC 1.00100 6.04754 0.76913 140.7349 469.1162
PM 5.01960 33.92487 83.80863 609.8511 609.8511
PP 10.57284 40.39489 57.20315 93.8232 93.8232
WF 2.53248 5.45694 4.94718 141.4292 258.7082
3586,3587c3587,3588
< x0 = 6.83298
< max sdi = 389.955
---
x0 = 6.83124
max sdi = 390.023
3589,3595c3590,3596
< CEIN 0.00000 8.76683 0.0000000 250.00000 250.00000
< COCO 0.00000 10.60933 0.0000000 825.00000 825.00000
< DF 6.22626 44.06074 3.2186911 15.22296 15.22296
< IC 1.20102 12.07219 0.0605327 7.69418 11.76394
< PM 4.84437 33.71814 2.0557684 16.06105 16.06105
< PP 11.29807 43.23521 9.0028449 12.93139 12.93139
< WF 3.77756 6.95055 0.3604408 4.63112 6.08461
---
CEIN 0.00000 8.74366 0.0000000 250.00000 250.00000
COCO 0.00000 10.61129 0.0000000 825.00000 825.00000
DF 6.24021 44.22627 3.2331328 15.22296 15.22296
IC 1.17869 11.77423 0.0583023 7.69418 11.76394
PM 4.84002 33.71119 2.0520768 16.06105 16.06105
PP 11.28971 43.23397 8.9895303 12.93139 12.93139
WF 3.77333 6.65046 0.3596351 4.63112 6.08461
3607,3608c3608,3609
< x0 = 6.83298
< max sdi = 380.894
---
x0 = 6.83124
max sdi = 380.956
3610,3611c3611,3612
< CEIN 0.0000 8.76683 0.00000 250.000000 250.000000
< COCO 0.0000 10.60933 0.00000 825.000000 825.000000
---
CEIN 0.00000 8.74366 0.00000 250.000000 250.000000
COCO 0.00000 10.61129 0.00000 825.000000 825.000000
3614,3616c3615,3617
< PM 5.4510 35.20515 10.65304 65.734863 65.734863
< PP 11.7561 44.51895 25.29875 33.561724 33.561724
< WF 35.2001 78.07525 4.69197 0.694292 0.694292
---
PM 5.44942 35.20515 10.64688 65.734863 65.734863
PP 11.72679 44.43688 25.17262 33.561724 33.561724
WF 35.20006 78.07609 4.69197 0.694292 0.694292
3627,3628c3628,3629
< x0 = 6.83298
< max sdi = 392.251
---
x0 = 6.83124
max sdi = 392.539
3630,3636c3631,3637
< CEIN 0.00000 8.76683 0.000000 250.0000 250.0000
< COCO 0.00000 10.60933 0.000000 825.0000 825.0000
< DF 3.14048 27.68502 21.449519 398.7488 398.7488
< IC 1.01997 6.15100 0.798552 140.7349 469.1162
< PM 5.20745 34.64782 16.639048 112.5000 112.5000
< PP 10.60746 40.60003 57.578321 93.8232 93.8232
< WF 2.53410 5.48953 4.953497 141.4292 258.7082
---
CEIN 0.00000 8.74366 0.00000 250.0000 250.0000
COCO 0.00000 10.61129 0.00000 825.0000 825.0000
DF 3.16517 28.02873 21.78805 398.7488 398.7488
IC 1.00100 6.04754 0.76913 140.7349 469.1162
PM 5.20398 34.64385 16.61688 112.5000 112.5000
PP 10.57284 40.39489 57.20315 93.8232 93.8232
WF 2.53248 5.45694 4.94718 141.4292 258.7082
3645c3646
< PM 0.1872181 0.7215733 -67.19049 -497.3511 -497.3511
---
PM 0.1843748 0.7189766 -67.19175 -497.3511 -497.3511
4375c4376
< max sdi = 398.846
---
max sdi = 398.41
4377,4383c4378,4384
< CEIN 0.00000 8.77646 0.00000 250.00 250.00
< COCO 0.00000 10.60993 0.00000 825.00 825.00
< DF 3.13603 27.61661 22.79684 425.00 425.00
< IC 1.04211 6.09452 0.88848 150.00 500.00
< PM 5.02090 33.92971 89.37223 650.00 650.00
< PP 10.51368 40.06350 60.28859 100.00 100.00
< WF 2.52873 5.30578 5.25726 150.74 275.74
---
CEIN 0.00000 8.77723 0.000000 250.00 250.00
COCO 0.00000 10.61171 0.000000 825.00 825.00
DF 3.14884 27.68445 22.983527 425.00 425.00
IC 1.00402 6.06886 0.824718 150.00 500.00
PM 5.01909 33.92520 89.307792 650.00 650.00
PP 10.64086 41.03086 61.755992 100.00 100.00
WF 2.53101 5.46218 5.266755 150.74 275.74
4403c4404
< max sdi = 392.643
---
max sdi = 392.207
4405,4411c4406,4412
< CEIN 0.00000 8.77646 0.00000 250.0000 250.0000
< COCO 0.00000 10.60993 0.00000 825.0000 825.0000
< DF 6.06295 42.12905 10.21732 50.9615 50.9615
< IC 1.04211 6.09452 0.88848 150.0000 500.0000
< PM 5.02090 33.92971 89.37223 650.0000 650.0000
< PP 10.51368 40.06350 60.28859 100.0000 100.0000
< WF 2.52873 5.30578 5.25726 150.7400 275.7400
---
CEIN 0.00000 8.77723 0.000000 250.0000 250.0000
COCO 0.00000 10.61171 0.000000 825.0000 825.0000
DF 6.09105 42.58754 10.312236 50.9615 50.9615
IC 1.00402 6.06886 0.824718 150.0000 500.0000
PM 5.01909 33.92520 89.307792 650.0000 650.0000
PP 10.64086 41.03086 61.755992 100.0000 100.0000
WF 2.53101 5.46218 5.266755 150.7400 275.7400
4423c4424
< max sdi = 389.885
---
max sdi = 389.775
4425,4431c4426,4432
< CEIN 0.00000 8.77646 0.0000000 250.00000 250.00000
< COCO 0.00000 10.60993 0.0000000 825.00000 825.00000
< DF 6.16773 43.35916 3.1584660 15.22296 15.22296
< IC 1.22710 11.95206 0.0631897 7.69418 11.76394
< PM 4.84963 33.73568 2.0602370 16.06105 16.06105
< PP 11.24155 42.89267 8.9129985 12.93139 12.93139
< WF 3.76924 6.14318 0.3588566 4.63112 6.08461
---
CEIN 0.00000 8.77723 0.0000000 250.00000 250.00000
COCO 0.00000 10.61171 0.0000000 825.00000 825.00000
DF 6.23059 44.06992 3.2231765 15.22296 15.22296
IC 1.18225 11.84774 0.0586553 7.69418 11.76394
PM 4.84046 33.71283 2.0524548 16.06105 16.06105
PP 11.35786 43.84667 9.0983840 12.93139 12.93139
WF 3.77715 6.98331 0.3603637 4.63112 6.08461
4443c4444
< max sdi = 380.596
---
max sdi = 380.196
4445,4446c4446,4447
< CEIN 0.00000 8.77646 0.00000 250.00 250.00
< COCO 0.00000 10.60993 0.00000 825.00 825.00
---
CEIN 0.00000 8.77723 0.00000 250.00 250.00
COCO 0.00000 10.61171 0.00000 825.00 825.00
4449,4451c4450,4452
< PM 5.45189 35.20515 12.15853 75.00 75.00
< PP 11.61414 43.44836 28.13313 38.24 38.24
< WF 35.20006 78.06928 5.00086 0.74 0.74
---
PM 5.45229 35.20515 12.16032 75.00 75.00
PP 11.80005 45.00217 29.04102 38.24 38.24
WF 35.20006 78.07701 5.00086 0.74 0.74
4463c4464
< max sdi = 392.417
---
max sdi = 392.047
4465,4471c4466,4472
< CEIN 0.00000 8.77646 0.00000 250.00 250.00
< COCO 0.00000 10.60993 0.00000 825.00 825.00
< DF 3.13603 27.61661 22.79684 425.00 425.00
< IC 1.04211 6.09452 0.88848 150.00 500.00
< PM 5.21096 34.65783 16.66151 112.50 112.50
< PP 10.51368 40.06350 60.28859 100.00 100.00
< WF 2.52873 5.30578 5.25726 150.74 275.74
---
CEIN 0.00000 8.77723 0.000000 250.00 250.00
COCO 0.00000 10.61171 0.000000 825.00 825.00
DF 3.14884 27.68445 22.983527 425.00 425.00
IC 1.00402 6.06886 0.824718 150.00 500.00
PM 5.20639 34.64478 16.632280 112.50 112.50
PP 10.64086 41.03086 61.755992 100.00 100.00
WF 2.53101 5.46218 5.266755 150.74 275.74
OK
* checking PDF version of manual ... OK
macbook:Desktop hamannjd$
I need to control the number of digits printed to remove the , but need to
focus on the max sdi values.
I'm assuming this is a 32/64-bit issue, but don't yet know how to control for
that.
Ideas?
Respectfully,
Jeff.
Jeff Hamann, PhD
PO Box 1421
Corvallis, Oregon 97339-1421
541-754-2457
jeff.hamann[at]forestinformatics[dot]com
jeff.d.hamann[at]gmail[dot]com
http://www.forestinformatics.com
http://en.wikipedia.org/wiki/Forest_informatics
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