* using log directory ‘/data/gannet/ripley/R/packages/tests-devel/supernova.Rcheck’
* using R Under development (unstable) (2025-02-15 r87723)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (GCC) 14.2.1 20240912 (Red Hat 14.2.1-3)
GNU Fortran (GCC) 14.2.1 20240912 (Red Hat 14.2.1-3)
* running under: Fedora Linux 40 (Workstation Edition)
* using session charset: UTF-8
* using option ‘--no-stop-on-test-error’
* checking for file ‘supernova/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘supernova’ version ‘3.0.0’
* 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 ‘supernova’ can be installed ... OK
See 'https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-fedora-gcc/supernova-00install.html' for details.
* 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 ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... OK
* checking use of S3 registration ... 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 ... [15s/20s] OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd line widths ... 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 examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... [79s/97s] ERROR
Running ‘testthat.R’ [78s/97s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(supernova)
>
> test_check("supernova")
Downloading GitHub repo UCLATALL/JMRData@HEAD
── R CMD build ─────────────────────────────────────────────────────────────────
* checking for file ‘/tmp/Rtmpb1oX7d/working_dir/RtmpCk6m1z/remotes8a8d75a0fc633/UCLATALL-JMRData-0b78ebe/DESCRIPTION’ ... OK
* preparing ‘JMRData’:
* checking DESCRIPTION meta-information ... OK
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* building ‘JMRData_0.1.0.tar.gz’
Installing package into '/data/gannet/ripley/R/packages/tests-devel/supernova.Rcheck'
(as 'lib' is unspecified)
* installing *source* package ‘JMRData’ ...
** this is package ‘JMRData’ version ‘0.1.0’
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (JMRData)
[ FAIL 4 | WARN 34 | SKIP 17 | PASS 232 ]
â•â• Skipped tests (17) 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•
• On CRAN (17): 'test-generate_models.R:222:3', 'test-listwise_delete.R:23:3',
'test-listwise_delete.R:29:3', 'test-listwise_delete.R:33:3',
'test-number.R:15:3', 'test-number.R:19:3', 'test-number.R:23:3',
'test-pairwise.R:18:3', 'test-pairwise.R:99:3', 'test-pairwise.R:113:3',
'test-supernova.lmerMod.R:150:3', 'test-supernova.lmerMod.R:164:3',
'test-supernova.r:321:3', 'test-supernova.r:333:3', 'test-supernova.r:338:3',
'test-supernova.r:343:3', 'test-supernova.r:348:3'
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-supernova.lmerMod.R:95:3'): supernova can test simple nested designs ──
supernova(model)$tbl (`actual`) not equal to `expected_jmr_ex11.1` (`expected`).
actual vs expected
SS MS F PRE p
- actual[1, ] 12.500 12.5000000 2.339181 0.3690037 0.2008918
+ expected[1, ] 12.500 12.5000000 4.686000 0.5400000 0.0960000
- actual[2, ] 21.375 5.3437500 NA NA NA
+ expected[2, ] 10.670 2.6700000 NA NA NA
- actual[3, ] 33.875 6.7750000 NA NA NA
+ expected[3, ] 23.170 4.6300000 NA NA NA
- actual[4, ] -5.375 -0.4479167 NA NA NA
+ expected[4, ] 5.330 0.4400000 NA NA NA
- actual[5, ] 28.500 1.6764706 NA NA NA
+ expected[5, ] 28.500 1.6800000 NA NA NA
`actual$SS`: 12.500 21.375 33.875 -5.375 28.500
`expected$SS`: 12.500 10.670 23.170 5.330 28.500
`actual$MS`: 12.500 5.344 6.775 -0.448 1.676
`expected$MS`: 12.500 2.670 4.630 0.440 1.680
`actual$F[1:4]`: 2.3 NA NA NA
`expected$F[1:4]`: 4.7 NA NA NA
`actual$PRE[1:4]`: 0.37 NA NA NA
`expected$PRE[1:4]`: 0.54 NA NA NA
`actual$p[1:4]`: 0.20 NA NA NA
`expected$p[1:4]`: 0.10 NA NA NA
── Failure ('test-supernova.lmerMod.R:108:3'): supernova can test simple crossed designs ──
supernova(model)$tbl (`actual`) not equal to `expected_jmr_ex11.9` (`expected`).
actual vs expected
SS MS F PRE p
- actual[1, ] 18.277439 2.6110627 NA NA NA
+ expected[1, ] 18.000000 2.5714000 NA NA NA
- actual[2, ] 2.250000 2.2500000 6.369914 0.4764364 0.03958605
+ expected[2, ] 2.250000 2.2500000 5.727000 0.4500000 0.04794000
- actual[3, ] 2.472561 0.3532230 NA NA NA
+ expected[3, ] 2.750000 0.3929000 NA NA NA
- actual[4, ] 4.722561 0.5903201 NA NA NA
+ expected[4, ] 5.000000 0.6250000 NA NA NA
- actual[5, ] 23.000000 1.5333333 NA NA NA
+ expected[5, ] 23.000000 1.5333000 NA NA NA
`actual$SS`: 18.2774 2.2500 2.4726 4.7226 23.0000
`expected$SS`: 18.0000 2.2500 2.7500 5.0000 23.0000
`actual$MS`: 2.6111 2.2500 0.3532 0.5903 1.5333
`expected$MS`: 2.5714 2.2500 0.3929 0.6250 1.5333
`actual$F`: NA 6.37 NA NA NA
`expected$F`: NA 5.73 NA NA NA
`actual$PRE`: NA 0.476 NA NA NA
`expected$PRE`: NA 0.450 NA NA NA
`actual$p`: NA 0.0396 NA NA NA
`expected$p`: NA 0.0479 NA NA NA
── Failure ('test-supernova.lmerMod.R:121:3'): supernova can test multiple crossed designs ──
supernova(model)$tbl (`actual`) not equal to `expected_jmr_ex11.17` (`expected`).
actual vs expected
SS MS F PRE p
- actual[1, ] 114.400000 28.6000000 NA NA NA
+ expected[1, ] 131.000000 32.7500000 NA NA NA
- actual[2, ] 65.866667 32.9333333 16.263374 0.8025995 0.001518423
+ expected[2, ] 65.870000 32.9300000 29.940000 0.8800000 0.000000000
- actual[3, ] 16.200000 2.0250000 NA NA NA
+ expected[3, ] 8.800000 1.1000000 NA NA NA
- actual[4, ] 17.633333 17.6333333 6.530864 0.6201641 0.062933674
+ expected[4, ] 17.630000 17.6300000 11.380000 0.7400000 0.028000000
- actual[5, ] 10.800000 2.7000000 NA NA NA
+ expected[5, ] 6.200000 1.5500000 NA NA NA
- actual[6, ] 1.866667 0.9333333 1.382716 0.2568807 0.304953824
+ expected[6, ] 1.870000 0.9300000 9.330000 0.7000000 0.008000000
- actual[7, ] 5.400000 0.6750000 NA NA NA
+ expected[7, ] 0.800000 0.1000000 NA NA NA
- actual[8, ] 117.766667 4.7106667 NA NA NA
+ expected[8, ] 101.170000 4.0500000 NA NA NA
- actual[9, ] 232.166667 8.0057471 NA NA NA
+ expected[9, ] 232.170000 8.0100000 NA NA NA
`actual$SS`: 114.400 65.867 16.200 17.633 10.800 1.867 5.400 117.767 232.167
`expected$SS`: 131.000 65.870 8.800 17.630 6.200 1.870 0.800 101.170 232.170
`actual$MS`: 28.600 32.933 2.025 17.633 2.700 0.933 0.675 4.711 8.006
`expected$MS`: 32.750 32.930 1.100 17.630 1.550 0.930 0.100 4.050 8.010
`actual$F`: NA 16.3 NA 6.5 NA 1.4 NA NA NA
`expected$F`: NA 29.9 NA 11.4 NA 9.3 NA NA NA
`actual$PRE`: NA 0.803 NA 0.620 NA 0.257 NA NA NA
`expected$PRE`: NA 0.880 NA 0.740 NA 0.700 NA NA NA
`actual$p`: NA 0.002 NA 0.063 NA 0.305 NA NA NA
`expected$p`: NA 0.000 NA 0.028 NA 0.008 NA NA NA
── Failure ('test-supernova.lmerMod.R:134:3'): supernova can test mixed designs ──
supernova(model)$tbl (`actual`) not equal to `expected_jmr_ex11.22` (`expected`).
actual vs expected
SS MS F PRE p
- actual[1, ] 10.125000 10.1250000 5.3435954 0.30810194 0.039360377
+ expected[1, ] 10.125000 10.1250000 9.5400000 0.44000000 0.009000000
- actual[2, ] 0.500000 0.5000000 0.2638813 0.02151694 0.616792935
+ expected[2, ] 0.500000 0.5000000 0.4800000 0.04000000 0.506000000
- actual[3, ] 10.125000 10.1250000 5.3435954 0.30810194 0.039360377
+ expected[3, ] 10.125000 10.1250000 9.5400000 0.44000000 0.009000000
- actual[4, ] 22.737500 1.8947917 NA NA NA
+ expected[4, ] 12.750000 1.0625000 NA NA NA
- actual[5, ] 43.487500 2.8991667 NA NA NA
+ expected[5, ] 33.500000 2.2333000 NA NA NA
- actual[6, ] 3.125000 3.1250000 12.6992853 0.51415598 0.003897925
+ expected[6, ] 3.125000 3.1250000 8.8200000 0.42000000 0.012000000
- actual[7, ] 2.000000 2.0000000 8.1275426 0.40380203 0.014598786
+ expected[7, ] 2.000000 2.0000000 5.6600000 0.32000000 0.035000000
- actual[8, ] 0.125000 0.1250000 0.5079714 0.04061181 0.489645842
+ expected[8, ] 0.125000 0.1250000 0.3500000 0.03000000 0.565000000
- actual[9, ] 0.500000 0.5000000 2.0318857 0.14480489 0.179518795
+ expected[9, ] 0.505000 0.5000000 1.4200000 0.11000000 0.256000000
- actual[10, ] 2.952922 0.2460768 NA NA NA
+ expected[10, ] 4.255000 0.3542000 NA NA NA
and 2 more ...
actual$SS | expected$SS
[1] 10.125 | 10.125 [1]
[2] 0.500 | 0.500 [2]
[3] 10.125 | 10.125 [3]
[4] 22.738 - 12.750 [4]
[5] 43.488 - 33.500 [5]
[6] 3.125 | 3.125 [6]
[7] 2.000 | 2.000 [7]
[8] 0.125 | 0.125 [8]
[9] 0.500 - 0.505 [9]
[10] 2.953 - 4.255 [10]
... ... ... and 2 more ...
actual$MS | expected$MS
[1] 10.125 | 10.125 [1]
[2] 0.500 | 0.500 [2]
[3] 10.125 | 10.125 [3]
[4] 1.895 - 1.062 [4]
[5] 2.899 - 2.233 [5]
[6] 3.125 | 3.125 [6]
[7] 2.000 | 2.000 [7]
[8] 0.125 | 0.125 [8]
[9] 0.500 | 0.500 [9]
[10] 0.246 - 0.354 [10]
... ... ... and 2 more ...
`actual$F`: 5.34 0.26 5.34 NA NA 12.70 8.13 0.51 2.03 NA and 2 more...
`expected$F`: 9.54 0.48 9.54 NA NA 8.82 5.66 0.35 1.42 NA ...
`actual$PRE`: 0.308 0.022 0.308 NA NA 0.514 0.404 0.041 0.145 NA and 2 more...
`expected$PRE`: 0.440 0.040 0.440 NA NA 0.420 0.320 0.030 0.110 NA ...
`actual$p`: 0.039 0.617 0.039 NA NA 0.004 0.015 0.490 0.180 NA and 2 more...
`expected$p`: 0.009 0.506 0.009 NA NA 0.012 0.035 0.565 0.256 NA ...
[ FAIL 4 | WARN 34 | SKIP 17 | PASS 232 ]
Deleting unused snapshots:
• pairwise/bonferroni-one-variable.svg
• pairwise/multiple-plots-term-factor-am.svg
• pairwise/multiple-plots-term-factor-cyl-factor-am.svg
• pairwise/t-test-one-variable.svg
Error: Test failures
Execution halted
* checking PDF version of manual ... OK
* checking HTML version of manual ... OK
* checking for non-standard things in the check directory ... NOTE
Found the following files/directories:
‘JMRData’
* checking for detritus in the temp directory ... OK
* DONE
Status: 1 ERROR, 1 NOTE