Last updated on 2025-02-26 14:54:11 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.0.3 | 7.36 | 179.62 | 186.98 | OK | |
| r-devel-linux-x86_64-debian-gcc | 1.0.3 | 5.34 | 124.67 | 130.01 | OK | |
| r-devel-linux-x86_64-fedora-clang | 1.0.3 | 281.55 | ERROR | |||
| r-devel-linux-x86_64-fedora-gcc | 1.0.3 | 292.98 | ERROR | |||
| r-devel-macos-arm64 | 1.0.3 | 93.00 | OK | |||
| r-devel-macos-x86_64 | 1.0.3 | 209.00 | OK | |||
| r-devel-windows-x86_64 | 1.0.3 | 14.00 | 210.00 | 224.00 | OK | |
| r-patched-linux-x86_64 | 1.0.3 | 8.34 | 174.53 | 182.87 | OK | |
| r-release-linux-x86_64 | 1.0.3 | 6.38 | 175.66 | 182.04 | OK | |
| r-release-macos-arm64 | 1.0.3 | 92.00 | OK | |||
| r-release-macos-x86_64 | 1.0.3 | 165.00 | OK | |||
| r-release-windows-x86_64 | 1.0.3 | 13.00 | 210.00 | 223.00 | OK | |
| r-oldrel-macos-arm64 | 1.0.3 | OK | ||||
| r-oldrel-macos-x86_64 | 1.0.3 | 175.00 | OK | |||
| r-oldrel-windows-x86_64 | 1.0.3 | 15.00 | 253.00 | 268.00 | OK |
Version: 1.0.3
Check: tests
Result: ERROR
Running ‘spelling.R’
Running ‘testthat.R’ [124s/142s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(cauphy)
Loading required package: ape
>
> test_check("cauphy")
[ FAIL 20 | WARN 2 | SKIP 0 | PASS 265 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('testAncestralStateReconstruction.R:148:3'): testAncestralFit ──────
MAP$par (`actual`) not equal to -0.5086788 (`expected`).
`actual`: -1.12
`expected`: -0.51
── Failure ('testCauchyLikelihood.R:258:3'): testLikelihoodFunction ────────────
ff$disp (`actual`) not equal to 0.06785236 (`expected`).
`actual`: 0.040
`expected`: 0.068
── Failure ('testFitFunctions.R:33:3'): optim ──────────────────────────────────
... <= res$logLik is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('testFitFunctions.R:41:3'): optim ──────────────────────────────────
unname(sqrt(diag(vcov(res)))) (`actual`) not equal to c(0.03243854, 0.0180895) (`expected`).
`actual`: 0.024 0.011
`expected`: 0.032 0.018
── Failure ('testFitFunctions.R:87:3'): optim, random root ─────────────────────
... <= res$logLik is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('testFitFunctions.R:100:3'): optim, random root ────────────────────
reslam$logLik > res$logLik is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('testFitFunctions.R:104:3'): optim, random root ────────────────────
unname(sqrt(diag(vcov(reslam)))) (`actual`) not equal to c(0.0285, 0.0415) (`expected`).
`actual`: NaN NaN
`expected`: 0.0 0.0
── Failure ('testFitFunctions.R:147:3'): optim, reml ───────────────────────────
... <= res$logLik is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('testFitFunctions.R:160:3'): optim, reml ───────────────────────────
unname(sqrt(diag(vcov(res)))) (`actual`) not equal to c(0.02016588) (`expected`).
`actual`: 0.008
`expected`: 0.020
── Failure ('testFitFunctions.R:164:3'): optim, reml ───────────────────────────
reslam$logLik > res$logLik is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('testFitFunctions.R:168:3'): optim, reml ───────────────────────────
unname(sqrt(diag(vcov(reslam)))) (`actual`) not equal to c(0.0283, 0.0574) (`expected`).
`actual`: NaN NaN
`expected`: 0.0 0.1
── Failure ('testFitFunctions.R:324:3'): cauphylm helper functions ─────────────
logLik(reslmdat) (`actual`) not equal to 13.296526 (`expected`).
`actual`: -Inf
`expected`: 13.3
── Failure ('testFitFunctions.R:325:3'): cauphylm helper functions ─────────────
AIC(reslmdat) (`actual`) not equal to -20.5930517 (`expected`).
`actual`: Inf
`expected`: -20.6
── Failure ('testFitFunctions.R:330:3'): cauphylm helper functions ─────────────
unname(sqrt(diag(vcov(reslmdat)))) (`actual`) not equal to c(0.04988679, 0.065175, 0.18057543) (`expected`).
`actual`: 0.030 0.035 0.303
`expected`: 0.050 0.065 0.181
── Failure ('testFitFunctions.R:390:3'): profile likelihood ────────────────────
max(pr$lambda$profLogLik) (`actual`) not equal to fit$logLik (`expected`).
`actual`: 12.6
`expected`: -Inf
── Failure ('testFitFunctions.R:391:3'): profile likelihood ────────────────────
mean(pr$x0$profLogLik) <= fit$logLik is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('testFitFunctions.R:392:3'): profile likelihood ────────────────────
mean(pr$disp$profLogLik) <= fit$logLik is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('testFitFunctions.R:393:3'): profile likelihood ────────────────────
mean(pr$lambda$profLogLik) <= fit$logLik is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('testIncrementReconstruction.R:206:3'): testAncestralIncrementFit ──
MAP$par (`actual`) not equal to 0.2811777 (`expected`).
`actual`: 0.48
`expected`: 0.28
── Failure ('testIncrementReconstruction.R:273:3'): testHDI ────────────────────
dim(hdi_all[[1]]) (`actual`) not equal to c(2, 2) (`expected`).
`actual`: 1.0 2.0
`expected`: 2.0 2.0
[ FAIL 20 | WARN 2 | SKIP 0 | PASS 265 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 1.0.3
Check: tests
Result: ERROR
Running ‘spelling.R’
Running ‘testthat.R’ [122s/146s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(cauphy)
Loading required package: ape
>
> test_check("cauphy")
[ FAIL 20 | WARN 2 | SKIP 0 | PASS 265 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('testAncestralStateReconstruction.R:148:3'): testAncestralFit ──────
MAP$par (`actual`) not equal to -0.5086788 (`expected`).
`actual`: -1.12
`expected`: -0.51
── Failure ('testCauchyLikelihood.R:258:3'): testLikelihoodFunction ────────────
ff$disp (`actual`) not equal to 0.06785236 (`expected`).
`actual`: 0.040
`expected`: 0.068
── Failure ('testFitFunctions.R:33:3'): optim ──────────────────────────────────
... <= res$logLik is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('testFitFunctions.R:41:3'): optim ──────────────────────────────────
unname(sqrt(diag(vcov(res)))) (`actual`) not equal to c(0.03243854, 0.0180895) (`expected`).
`actual`: 0.024 0.011
`expected`: 0.032 0.018
── Failure ('testFitFunctions.R:87:3'): optim, random root ─────────────────────
... <= res$logLik is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('testFitFunctions.R:100:3'): optim, random root ────────────────────
reslam$logLik > res$logLik is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('testFitFunctions.R:104:3'): optim, random root ────────────────────
unname(sqrt(diag(vcov(reslam)))) (`actual`) not equal to c(0.0285, 0.0415) (`expected`).
`actual`: NaN NaN
`expected`: 0.0 0.0
── Failure ('testFitFunctions.R:147:3'): optim, reml ───────────────────────────
... <= res$logLik is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('testFitFunctions.R:160:3'): optim, reml ───────────────────────────
unname(sqrt(diag(vcov(res)))) (`actual`) not equal to c(0.02016588) (`expected`).
`actual`: 0.008
`expected`: 0.020
── Failure ('testFitFunctions.R:164:3'): optim, reml ───────────────────────────
reslam$logLik > res$logLik is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('testFitFunctions.R:168:3'): optim, reml ───────────────────────────
unname(sqrt(diag(vcov(reslam)))) (`actual`) not equal to c(0.0283, 0.0574) (`expected`).
`actual`: NaN NaN
`expected`: 0.0 0.1
── Failure ('testFitFunctions.R:324:3'): cauphylm helper functions ─────────────
logLik(reslmdat) (`actual`) not equal to 13.296526 (`expected`).
`actual`: -Inf
`expected`: 13.3
── Failure ('testFitFunctions.R:325:3'): cauphylm helper functions ─────────────
AIC(reslmdat) (`actual`) not equal to -20.5930517 (`expected`).
`actual`: Inf
`expected`: -20.6
── Failure ('testFitFunctions.R:330:3'): cauphylm helper functions ─────────────
unname(sqrt(diag(vcov(reslmdat)))) (`actual`) not equal to c(0.04988679, 0.065175, 0.18057543) (`expected`).
`actual`: 0.030 0.035 0.303
`expected`: 0.050 0.065 0.181
── Failure ('testFitFunctions.R:390:3'): profile likelihood ────────────────────
max(pr$lambda$profLogLik) (`actual`) not equal to fit$logLik (`expected`).
`actual`: 12.6
`expected`: -Inf
── Failure ('testFitFunctions.R:391:3'): profile likelihood ────────────────────
mean(pr$x0$profLogLik) <= fit$logLik is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('testFitFunctions.R:392:3'): profile likelihood ────────────────────
mean(pr$disp$profLogLik) <= fit$logLik is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('testFitFunctions.R:393:3'): profile likelihood ────────────────────
mean(pr$lambda$profLogLik) <= fit$logLik is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('testIncrementReconstruction.R:206:3'): testAncestralIncrementFit ──
MAP$par (`actual`) not equal to 0.2811777 (`expected`).
`actual`: 0.48
`expected`: 0.28
── Failure ('testIncrementReconstruction.R:273:3'): testHDI ────────────────────
dim(hdi_all[[1]]) (`actual`) not equal to c(2, 2) (`expected`).
`actual`: 1.0 2.0
`expected`: 2.0 2.0
[ FAIL 20 | WARN 2 | SKIP 0 | PASS 265 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc