Last updated on 2026-04-24 06:52:57 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.5 | 370.25 | 275.27 | 645.52 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 1.5.1 | 271.14 | 185.82 | 456.96 | OK | |
| r-devel-linux-x86_64-fedora-clang | 1.5.1 | 480.00 | 373.16 | 853.16 | OK | |
| r-devel-linux-x86_64-fedora-gcc | 1.5.1 | 840.00 | 366.53 | 1206.53 | OK | |
| r-devel-macos-arm64 | 1.5.1 | 8.00 | -1.00 | 7.00 | ERROR | |
| r-devel-windows-x86_64 | 1.5.1 | 277.00 | 289.00 | 566.00 | OK | |
| r-patched-linux-x86_64 | 1.5 | 363.32 | 254.76 | 618.08 | OK | |
| r-release-linux-x86_64 | 1.5 | 374.24 | 240.13 | 614.37 | OK | |
| r-release-macos-arm64 | 1.5.1 | 74.00 | 16.00 | 90.00 | OK | |
| r-release-macos-x86_64 | 1.5.1 | 293.00 | 292.00 | 585.00 | OK | |
| r-release-windows-x86_64 | 1.5.1 | 261.00 | 367.00 | 628.00 | OK | |
| r-oldrel-macos-arm64 | 1.4.10 | 79.00 | 15.00 | 94.00 | NOTE | |
| r-oldrel-macos-x86_64 | 1.5.1 | 283.00 | 314.00 | 597.00 | NOTE | |
| r-oldrel-windows-x86_64 | 1.5.1 | 290.00 | 348.00 | 638.00 | NOTE |
Version: 1.5
Check: tests
Result: ERROR
Running ‘spelling.R’ [0s/0s]
Running ‘testthat.R’ [89s/113s]
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/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
>
> library(testthat)
> library(Colossus)
>
> test_check("Colossus")
Saving _problems/test-CaseControl-72.R
Saving _problems/test-CaseControl-72.R
Saving _problems/test-CaseControl-223.R
Saving _problems/test-CaseControl-223.R
Saving _problems/test-CaseControl-223.R
Saving _problems/test-CaseControl-223.R
Saving _problems/test-CaseControl-242.R
Saving _problems/test-CaseControl-344.R
Saving _problems/test-CaseControl-345.R
Saving _problems/test-CaseControl-349.R
Saving _problems/test-CaseControl-350.R
Saving _problems/test-CaseControl-351.R
Saving _problems/test-CaseControl-352.R
Saving _problems/test-CaseControl-349.R
Saving _problems/test-CaseControl-350.R
Saving _problems/test-CaseControl-351.R
Saving _problems/test-CaseControl-352.R
Saving _problems/test-CaseControl-363.R
Saving _problems/test-CaseControl-364.R
Saving _problems/test-CaseControl-366.R
Saving _problems/test-CoxPlot-154.R
Saving _problems/test-CoxRegression-118.R
Saving _problems/test-CoxRegression-163.R
Saving _problems/test-Formula-176.R
Saving _problems/test-Gradient-63.R
Saving _problems/test-Gradient-135.R
Saving _problems/test-Norm-58.R
Saving _problems/test-Norm-61.R
Saving _problems/test-Norm-58.R
Saving _problems/test-Norm-61.R
Saving _problems/test-Norm-67.R
Saving _problems/test-Norm-67.R
Saving _problems/test-Omnibus-366.R
Saving _problems/test-Utility-170.R
Saving _problems/test-Utility-171.R
[ FAIL 35 | WARN 12 | SKIP 15 | PASS 825 ]
══ Skipped tests (15) ══════════════════════════════════════════════════════════
• Cran Skip (15): 'test-Assigned.R:74:5', 'test-CoxRegression.R:215:5',
'test-Logbound.R:24:5', 'test-Logbound.R:110:5', 'test-Logbound.R:161:5',
'test-Logbound.R:203:5', 'test-Logbound.R:251:5', 'test-Logbound.R:329:5',
'test-Logbound.R:357:5', 'test-Omnibus.R:21:5', 'test-Omnibus.R:67:5',
'test-Omnibus.R:147:5', 'test-Omnibus.R:214:5', 'test-Omnibus.R:256:5',
'test-Omnibus.R:453:5'
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-CaseControl.R:72:11'): threshold nonfail ─────────────────────
Expected `e$Deviation` to equal `devs[i_index]`.
Differences:
`actual`: 850.9
`expected`: 847.1
── Failure ('test-CaseControl.R:72:11'): threshold nonfail ─────────────────────
Expected `e$Deviation` to equal `devs[i_index]`.
Differences:
`actual`: 62.1
`expected`: 63.5
── Failure ('test-CaseControl.R:223:13'): threshold nonfail, gradient ──────────
Expected `e$Deviation` to equal `devs[i_index]`.
Differences:
`actual`: 1001.9
`expected`: 2365.3
── Failure ('test-CaseControl.R:223:13'): threshold nonfail, gradient ──────────
Expected `e$Deviation` to equal `devs[i_index]`.
Differences:
`actual`: 620.3
`expected`: 645.8
── Failure ('test-CaseControl.R:223:13'): threshold nonfail, gradient ──────────
Expected `e$Deviation` to equal `devs[i_index]`.
Differences:
`actual`: 732.7
`expected`: 662.9
── Failure ('test-CaseControl.R:223:13'): threshold nonfail, gradient ──────────
Expected `e$Deviation` to equal `devs[i_index]`.
Differences:
`actual`: 898.3
`expected`: 645.8
── Failure ('test-CaseControl.R:242:13'): threshold nonfail, gradient ──────────
Expected `e$Deviation` to equal `devs[i_index]`.
Differences:
`actual`: 962.7
`expected`: 961.7
── Failure ('test-CaseControl.R:344:7'): information matrix calculations ───────
Expected `ee$Standard_Deviation[1]` to equal `model0_sde[i_index]`.
Differences:
`actual`: 0.01406
`expected`: 0.01403
── Failure ('test-CaseControl.R:345:7'): information matrix calculations ───────
Expected `ee$Standard_Deviation[2]` to equal `model0_sde[i_index + 1]`.
Differences:
`actual`: 0.4912
`expected`: 0.4901
── Failure ('test-CaseControl.R:349:7'): information matrix calculations ───────
Expected `eo$Standard_Deviation[1]` to equal `model1_sdo[i_index]`.
Differences:
`actual`: 0.0161
`expected`: 0.0138
── Failure ('test-CaseControl.R:350:7'): information matrix calculations ───────
Expected `eo$Standard_Deviation[2]` to equal `model1_sdo[i_index + 1]`.
Differences:
`actual`: 0.371
`expected`: 0.432
── Failure ('test-CaseControl.R:351:7'): information matrix calculations ───────
Expected `ee$Standard_Deviation[1]` to equal `model1_sde[i_index]`.
Differences:
`actual`: 0.01353
`expected`: 0.01406
── Failure ('test-CaseControl.R:352:7'): information matrix calculations ───────
Expected `ee$Standard_Deviation[2]` to equal `model1_sde[i_index + 1]`.
Differences:
`actual`: 0.48189
`expected`: 0.48225
── Failure ('test-CaseControl.R:349:7'): information matrix calculations ───────
Expected `eo$Standard_Deviation[1]` to equal `model1_sdo[i_index]`.
Differences:
`actual`: 0.0164
`expected`: 0.0232
── Failure ('test-CaseControl.R:350:7'): information matrix calculations ───────
Expected `eo$Standard_Deviation[2]` to equal `model1_sdo[i_index + 1]`.
Differences:
`actual`: 0.36
`expected`: 0.51
── Failure ('test-CaseControl.R:351:7'): information matrix calculations ───────
Expected `ee$Standard_Deviation[1]` to equal `model1_sde[i_index]`.
Differences:
`actual`: 0.0164
`expected`: 0.0232
── Failure ('test-CaseControl.R:352:7'): information matrix calculations ───────
Expected `ee$Standard_Deviation[2]` to equal `model1_sde[i_index + 1]`.
Differences:
`actual`: 0.36
`expected`: 0.51
── Failure ('test-CaseControl.R:363:7'): information matrix calculations ───────
Expected `eo$Standard_Deviation[1]` to equal `model3_sdo[i_index]`.
Differences:
`actual`: 0.0039
`expected`: 0.0056
── Failure ('test-CaseControl.R:364:7'): information matrix calculations ───────
Expected `eo$Standard_Deviation[2]` to equal `model3_sdo[i_index + 1]`.
Differences:
`actual`: 0.114
`expected`: 0.161
── Failure ('test-CaseControl.R:366:7'): information matrix calculations ───────
Expected `ee$Standard_Deviation[2]` to equal `model3_sde[i_index + 1]`.
Differences:
`actual`: 0.16085
`expected`: 0.16083
── Failure ('test-CoxPlot.R:154:5'): Coxph risk plotting above discrete step number limit ──
Expected `ep$y[100]` to equal 0.9938494.
Differences:
`actual`: 0.976
`expected`: 0.994
── Failure ('test-CoxRegression.R:118:3'): Coxph dose list ─────────────────────
Expected `e$beta_0` to equal `c(...)`.
Differences:
actual | expected
[1] 1.000 | 1.000 [1]
[2] -0.037 - -0.088 [2]
[3] -0.065 - -0.090 [3]
[4] 0.598 - 0.991 [4]
[5] -0.120 - -0.053 [5]
[6] 1.126 - 1.119 [6]
[7] 3.057 - 2.942 [7]
[8] 0.175 - 0.107 [8]
[9] 0.232 - 1.573 [9]
[10] 0.300 - 0.301 [10]
... ... ... and 2 more ...
── Failure ('test-CoxRegression.R:163:3'): Coxph loglin_M Null ─────────────────
Expected `e$AIC` to equal 1052.
Differences:
`actual`: 2103.1
`expected`: 1052.0
── Failure ('test-Formula.R:176:3'): Checking formula works with result modification ──
Expected `sum(f$Risk)` to equal 548.6874.
Differences:
`actual`: 858.2
`expected`: 548.7
── Failure ('test-Gradient.R:63:3'): Coxph gradient methods ────────────────────
Expected `e2$beta_0` to equal `c(0.6594536, 0.7276018)`.
Differences:
`actual`: 0.6585 0.7271
`expected`: 0.6595 0.7276
── Failure ('test-Gradient.R:135:5'): Constraint Check ─────────────────────────
Expected `e4$beta_0` to equal `c(0.04037, -0.04037)`.
Differences:
`actual`: 0.0402 -0.0402
`expected`: 0.0404 -0.0404
── Failure ('test-Norm.R:58:7'): Checking values converted back ────────────────
Expected `res$First_Der` to equal `res_max$First_Der`.
Differences:
`actual`: 3218.9 -15.2
`expected`: 1609.4 -7.6
── Failure ('test-Norm.R:61:7'): Checking values converted back ────────────────
Expected `res$Second_Der` to equal `res_max$Second_Der`.
Differences:
actual vs expected
[,1] [,2]
- actual[1, ] -30854.26606 -26.77289
+ expected[1, ] -15427.13303 -13.38645
- actual[2, ] -26.77289 -38.54087
+ expected[2, ] -13.38645 -19.27044
── Failure ('test-Norm.R:58:7'): Checking values converted back ────────────────
Expected `res$First_Der` to equal `res_max$First_Der`.
Differences:
`actual`: -15.6 -6.4
`expected`: -31.3 -12.8
── Failure ('test-Norm.R:61:7'): Checking values converted back ────────────────
Expected `res$Second_Der` to equal `res_max$Second_Der`.
Differences:
actual vs expected
[,1] [,2]
- actual[1, ] -32778.82740 15.26637
+ expected[1, ] -65557.65480 30.53274
- actual[2, ] 15.26637 -24.61536
+ expected[2, ] 30.53274 -49.23072
── Failure ('test-Norm.R:67:7'): Checking values converted back ────────────────
Expected `res$Standard_Deviation` to equal `res_max$Standard_Deviation`.
Differences:
`actual`: 0.006 0.202
`expected`: 0.004 0.143
── Failure ('test-Norm.R:67:7'): Checking values converted back ────────────────
Expected `res$Standard_Deviation` to equal `res_max$Standard_Deviation`.
Differences:
`actual`: 0.007 0.203
`expected`: 0.005 0.144
── Failure ('test-Omnibus.R:366:3'): check deviation calc, expected cox ────────
Expected `devs` to equal `c(...)`.
Differences:
`actual`: 0.43448 0.38255 0.52225 0.67186 0.45005 0.56292 0.73815 0.97195
`expected`: 0.61445 0.54101 0.73858 0.95015 0.63646 0.56292 0.73815 0.97195
── Failure ('test-Utility.R:170:3'): Improve Ratio test ────────────────────────
Expected `val$Difference` to equal 2.200062.
Differences:
`actual`: 5.9
`expected`: 2.2
── Failure ('test-Utility.R:171:3'): Improve Ratio test ────────────────────────
Expected `val$"p value"` to equal 0.5319362.
Differences:
`actual`: 0.12
`expected`: 0.53
[ FAIL 35 | WARN 12 | SKIP 15 | PASS 825 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang
Version: 1.5.1
Check: whether package can be installed
Result: ERROR
Installation failed.
Flavor: r-devel-macos-arm64
Version: 1.4.10
Check: installed package size
Result: NOTE
installed size is 105.8Mb
sub-directories of 1Mb or more:
doc 1.7Mb
libs 103.5Mb
Flavor: r-oldrel-macos-arm64
Version: 1.5.1
Check: installed package size
Result: NOTE
installed size is 110.1Mb
sub-directories of 1Mb or more:
doc 1.7Mb
libs 107.8Mb
Flavors: r-oldrel-macos-x86_64, r-oldrel-windows-x86_64
Version: 1.5.1
Check: R code for possible problems
Result: NOTE
EventAssignment.poisres: no visible global function definition for
‘grepv’
EventAssignment.poisresbound: no visible global function definition for
‘grepv’
LikelihoodBound.coxres: no visible global function definition for
‘grepv’
LikelihoodBound.poisres: no visible global function definition for
‘grepv’
RelativeRisk.coxres: no visible global function definition for ‘grepv’
Residual.poisres: no visible global function definition for ‘grepv’
plot.coxres: no visible global function definition for ‘grepv’
Undefined global functions or variables:
grepv
Flavors: r-oldrel-macos-x86_64, r-oldrel-windows-x86_64