* using log directory ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.5/bdsm.Rcheck’
* using R Under development (unstable) (2025-02-02 r87676)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.3.1
* using session charset: UTF-8
* checking for file ‘bdsm/DESCRIPTION’ ... OK
* this is package ‘bdsm’ version ‘0.1.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘bdsm’ can be installed ... [3s/4s] OK
See 'https://www.r-project.org/nosvn/R.check/r-devel-macos-x86_64/bdsm-00install.html' for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [1s/1s] OK
* checking whether the package can be loaded with stated dependencies ... [0s/1s] OK
* checking whether the package can be unloaded cleanly ... [0s/0s] OK
* checking whether the namespace can be loaded with stated dependencies ... [0s/0s] OK
* checking whether the namespace can be unloaded cleanly ... [1s/1s] OK
* checking loading without being on the library search path ... [1s/1s] OK
* checking 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 ... [3s/4s] OK
* checking Rd files ... [0s/0s] 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 ... [0s/0s] OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking examples ... [2s/2s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... [268s/380s] ERROR
Running ‘testthat.R’ [267s/380s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
>
> library(testthat)
> library(bdsm)
>
> test_check("bdsm")
[1] "Prior Mean Model Size: 2"
[1] "Prior Inclusion Probability: 0.5"
[1] "Prior Mean Model Size: 2"
[1] "Prior Inclusion Probability: 0.5"
[1] "Posterior Mean Model Size: 4.08027539207968"
initial value 683.117366
iter 100 value 41.336092
final value 39.044737
converged
initial value 741.819590
iter 100 value -32.153775
final value -33.313975
converged
initial value 715.204410
iter 100 value -29.034048
final value -30.705138
converged
initial value 854.010861
iter 100 value -99.535858
final value -104.715978
converged
initial value 802.489421
iter 100 value -12.381517
final value -13.889648
converged
initial value 773.966583
iter 100 value -83.238184
final value -86.195425
converged
initial value 730.140223
iter 100 value -72.197310
final value -82.124903
converged
initial value 779.593030
iter 100 value -150.585450
final value -155.702262
converged
initial value 646.828778
iter 100 value -276.660860
final value -280.031940
converged
initial value 693.058877
iter 100 value -348.970387
final value -352.097641
converged
initial value 661.565114
iter 100 value -332.294744
final value -346.967522
converged
initial value 788.861127
iter 100 value -410.642350
final value -420.960599
converged
initial value 730.184924
iter 100 value -322.602127
final value -332.946427
converged
initial value 693.137385
iter 100 value -397.149571
final value -404.867446
converged
initial value 642.628746
iter 100 value -384.562963
final value -398.464515
converged
initial value 686.560634
iter 100 value -460.244828
final value -472.282810
converged
[ FAIL 7 | WARN 1 | SKIP 0 | PASS 14 ]
â•â• Failed tests â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•
── Failure ('test-SEM_bma.R:40:3'): parameters_summary computes correct approximations of BMA parameters of interest based on economic_growth_ms ──
`bma_params` (`actual`) not equal to `economic_growth_bma_params` (`expected`).
actual vs expected
postprob pmean std stdR unc_pmean unc_std unc_stdR
- actual[1, ] 1 1.00829454294323 0.109017126815034 0.160909304579616 1.00829454294323 0.109017126815034 0.160909304579616
+ expected[1, ] 1 1.00829454294324 0.109017116430091 0.160909279425281 1.00829454294324 0.109017116430091 0.160909279425281
- actual[2, ] 0.72421542903605 0.112526720636743 0.0290170260380944 0.0713066024147719 0.0814935872639584 0.0560248330517665 0.0788122451181888
+ expected[2, ] 0.724215429035913 0.112526720636744 0.02901702834219 0.0713066112642638 0.0814935872639437 0.0560248339160252 0.0788122509167764
- actual[3, ] 0.707755014395393 -0.000586362187472065 0.0599963932657828 0.0972102314804381 -0.000415000778435205 0.0504745763136361 0.0817816302661768
+ expected[3, ] 0.707755014395517 -0.000586362187470274 0.0599963866181173 0.097210204697469 -0.000415000778434011 0.0504745707211588 0.0817816077342801
- actual[4, ] 0.661624225314199 -0.0256807724665409 0.0370901929747144 0.0832530530286312 -0.0169910211886454 0.0325243379659662 0.0687997973998867
+ expected[4, ] 0.661624225314061 -0.0256807724665425 0.0370901934868091 0.0832530514935827 -0.0169910211886429 0.0325243383523419 0.0687997961708953
- actual[5, ] 0.986680723334034 0.131098360731761 0.0472864728729402 0.0620826414199004 0.12935222539472 0.0493162748567766 0.063472710491369
+ expected[5, ] 0.986680723334043 0.131098360731763 0.0472864706556068 0.0620826347252909 0.129352225394724 0.0493162727590226 0.0634727040305869
actual$postprob | expected$postprob
[1] "1" | "1" [1]
[2] "0.72421542903605" - "0.724215429035913" [2]
[3] "0.707755014395393" - "0.707755014395517" [3]
[4] "0.661624225314199" - "0.661624225314061" [4]
[5] "0.986680723334034" - "0.986680723334043" [5]
actual$pmean | expected$pmean
[1] "1.00829454294323" - "1.00829454294324" [1]
[2] "0.112526720636743" - "0.112526720636744" [2]
[3] "-0.000586362187472065" - "-0.000586362187470274" [3]
[4] "-0.0256807724665409" - "-0.0256807724665425" [4]
[5] "0.131098360731761" - "0.131098360731763" [5]
actual$std | expected$std
[1] "0.109017126815034" - "0.109017116430091" [1]
[2] "0.0290170260380944" - "0.02901702834219" [2]
[3] "0.0599963932657828" - "0.0599963866181173" [3]
[4] "0.0370901929747144" - "0.0370901934868091" [4]
[5] "0.0472864728729402" - "0.0472864706556068" [5]
actual$stdR | expected$stdR
[1] "0.160909304579616" - "0.160909279425281" [1]
[2] "0.0713066024147719" - "0.0713066112642638" [2]
[3] "0.0972102314804381" - "0.097210204697469" [3]
[4] "0.0832530530286312" - "0.0832530514935827" [4]
[5] "0.0620826414199004" - "0.0620826347252909" [5]
actual$unc_pmean | expected$unc_pmean
[1] "1.00829454294323" - "1.00829454294324" [1]
[2] "0.0814935872639584" - "0.0814935872639437" [2]
[3] "-0.000415000778435205" - "-0.000415000778434011" [3]
[4] "-0.0169910211886454" - "-0.0169910211886429" [4]
[5] "0.12935222539472" - "0.129352225394724" [5]
actual$unc_std | expected$unc_std
[1] "0.109017126815034" - "0.109017116430091" [1]
[2] "0.0560248330517665" - "0.0560248339160252" [2]
[3] "0.0504745763136361" - "0.0504745707211588" [3]
[4] "0.0325243379659662" - "0.0325243383523419" [4]
[5] "0.0493162748567766" - "0.0493162727590226" [5]
actual$unc_stdR | expected$unc_stdR
[1] "0.160909304579616" - "0.160909279425281" [1]
[2] "0.0788122451181888" - "0.0788122509167764" [2]
[3] "0.0817816302661768" - "0.0817816077342801" [3]
[4] "0.0687997973998867" - "0.0687997961708953" [4]
[5] "0.063472710491369" - "0.0634727040305869" [5]
── Failure ('test-SEM_likelihood.R:20:3'): SEM likelihood is calculated correctly for default feature standardization parameters ──
`sem_value` (`actual`) not equal to 133.223858 (`expected`).
`actual`: 134.05
`expected`: 133.22
── Failure ('test-SEM_likelihood.R:31:3'): SEM likelihood is calculated correctly for cross_sectional TRUE ──
`sem_value` (`actual`) not equal to 217.693805 (`expected`).
`actual`: NaN
`expected`: 217.7
── Failure ('test-SEM_likelihood.R:42:3'): SEM likelihood is calculated correctly for cross_sectional TRUE and scale FALSE ──
`sem_value` (`actual`) not equal to 225.54665 (`expected`).
`actual`: 220.8
`expected`: 225.5
── Failure ('test-SEM_likelihood.R:53:3'): SEM likelihood is calculated correctly for cross_sectional FALSE and scale FALSE ──
`sem_value` (`actual`) not equal to 140.498138 (`expected`).
`actual`: 137.7
`expected`: 140.5
── Failure ('test-SEM_likelihood.R:60:3'): SEM likelihood is calculated incorrectly for specific data ──
`... <- NULL` did not throw the expected warning.
── Failure ('test-model_space.R:14:3'): optimal_model_space correctly computes economic_growth_ms ──
`model_space` (`actual`) not equal to `economic_growth_ms` (`expected`).
actual vs expected
[, 1] [, 2] [, 3] [, 4] [, 5] [, 6] [, 7] [, 8] [, 9] [,10] [,11] [,12] [,13] [,14] [,15] [,16]
- actual[1, ] 1.1407325063 1.099698e+00 1.219560e+00 1.127542e+00 1.1279671582 1.058458e+00 1.199070e+00 1.093936e+00 1.0229286469 9.907342e-01 1.026809e+00 9.910167e-01 1.0215222881 9.825492e-01 1.0642556470 0.9993842297
+ expected[1, ] 1.1407202923 1.099688e+00 1.219552e+00 1.127555e+00 1.1279645652 1.058468e+00 1.199063e+00 1.093931e+00 1.0229544660 9.907199e-01 1.027003e+00 9.910331e-01 1.0214418175 9.825608e-01 1.0638442494 0.9990677746
- actual[2, ] -0.1337837871 -1.234192e-01 -2.238277e-01 -1.571172e-01 -0.1523512563 -1.016383e-01 -2.176306e-01 -1.337998e-01 0.0052956338 2.742419e-04 -2.919798e-02 -2.361047e-02 -0.0246056328 -1.277954e-02 -0.0794821380 -0.0414361219
+ expected[2, ] -0.1337698199 -1.234106e-01 -2.238198e-01 -1.571318e-01 -0.1523512071 -1.016449e-01 -2.176220e-01 -1.337997e-01 0.0052687351 2.944010e-04 -2.933656e-02 -2.364125e-02 -0.0245075902 -1.279735e-02 -0.0790667316 -0.0411687979
- actual[3, ] 0.0566501922 9.004261e-06 2.966200e-02 -7.925328e-06 0.0315549903 -2.007114e-06 1.494634e-05 5.104379e-06 0.0808146797 5.441573e-02 7.512395e-02 4.901756e-02 0.0651825858 4.284459e-02 0.0498885060 0.0330727204
+ expected[3, ] 0.0566618039 -2.723644e-06 2.966844e-02 1.926969e-06 0.0315501147 -5.724588e-06 -2.503582e-06 6.775119e-07 0.0808056570 5.441414e-02 7.513490e-02 4.900858e-02 0.0652042724 4.284360e-02 0.0500775664 0.0332238513
- actual[4, ] 0.1870429391 1.579152e-01 1.862188e-01 1.572039e-01 0.1832583712 1.552333e-01 1.809164e-01 1.540559e-01 0.1753577559 1.487462e-01 1.764188e-01 1.512840e-01 0.1732439844 1.483854e-01 0.1759379410 0.1510929710
+ expected[4, ] 0.1870405168 1.579151e-01 1.862189e-01 1.572051e-01 0.1832570668 1.552363e-01 1.809174e-01 1.540587e-01 0.1753630868 1.487515e-01 1.764077e-01 1.512714e-01 0.1732270130 1.483862e-01 0.1758809678 0.1510713715
- actual[5, ] 0.1789097102 1.831147e-01 1.879526e-01 1.853265e-01 0.1812605183 1.785085e-01 1.883520e-01 1.819459e-01 0.1592329556 1.653235e-01 1.591877e-01 1.651138e-01 -0.1625687606 1.651813e-01 0.1674691404 -0.1672718522
+ expected[5, ] 0.1789069659 1.831147e-01 1.879514e-01 1.853255e-01 0.1812617190 1.785093e-01 1.883498e-01 1.819451e-01 0.1592365100 1.653227e-01 1.592308e-01 1.651126e-01 -0.1625563946 1.651936e-01 0.1674196084 -0.1672350885
- actual[6, ] 0.1652244128 1.698859e-01 1.708075e-01 1.692047e-01 0.1650784078 1.636737e-01 1.692961e-01 1.635205e-01 0.1550105251 1.588088e-01 1.551735e-01 1.590770e-01 0.1540452698 1.564201e-01 0.1567670034 0.1574173497
+ expected[6, ] 0.1652207814 1.698873e-01 1.708065e-01 1.692045e-01 0.1650800163 1.636750e-01 1.692969e-01 1.635208e-01 0.1550156414 1.587944e-01 1.551830e-01 1.591196e-01 0.1540451252 1.564180e-01 0.1567235451 0.1573871196
- actual[7, ] -0.1520433611 1.588928e-01 1.646212e-01 1.623433e-01 0.1504663184 1.498382e-01 1.629938e-01 1.545332e-01 0.1357682693 1.380035e-01 1.359455e-01 1.375993e-01 0.1357166752 1.360004e-01 0.1394915401 0.1373896493
+ expected[7, ] -0.1520419424 1.588954e-01 1.646199e-01 1.623447e-01 0.1504677299 1.498407e-01 1.629930e-01 1.545342e-01 0.1357717573 1.380062e-01 1.359649e-01 1.376105e-01 0.1357089321 1.360063e-01 0.1394476198 0.1373489242
- actual[8, ] NA 1.324415e-01 NA 1.285602e-01 NA 1.239101e-01 NA 1.192018e-01 NA 1.113466e-01 NA 1.150299e-01 NA 1.086973e-01 NA 0.1127648324
+ expected[8, ] NA 1.324535e-01 NA 1.285555e-01 NA 1.239084e-01 NA 1.192009e-01 NA 1.113591e-01 NA 1.150310e-01 NA 1.086753e-01 NA 0.1127508358
- actual[9, ] NA NA -7.944206e-02 -5.768929e-02 NA NA -1.044436e-01 -7.058526e-02 NA NA 8.454603e-04 1.697146e-02 NA NA -0.0250838336 0.0012951342
+ expected[9, ] NA NA -7.944448e-02 -5.769177e-02 NA NA -1.044348e-01 -7.058320e-02 NA NA 5.974547e-04 1.699712e-02 NA NA -0.0250275552 0.0014754601
- actual[10, ] NA NA NA NA -0.0411337531 -2.456049e-02 -5.480890e-02 -3.198520e-02 NA NA NA NA -0.0259843783 -2.080769e-02 -0.0345857902 -0.0240797851
+ expected[10, ] NA NA NA NA -0.0411431305 -2.455238e-02 -5.480525e-02 -3.198845e-02 NA NA NA NA -0.0259939837 -2.081871e-02 -0.0345197432 -0.0240326129
and 41 more ...
[ FAIL 7 | WARN 1 | SKIP 0 | PASS 14 ]
Error: Test failures
Execution halted
* checking PDF version of manual ... [7s/7s] OK
* DONE
Status: 1 ERROR
* using check arguments '--no-clean-on-error '
* elapsed time (check, wall clock): 6:58