• using R Under development (unstable) (2026-04-19 r89916)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     Debian clang version 21.1.8 (3+b1)     Debian flang version 21.1.8 (3+b1)
• running under: Debian GNU/Linux forky/sid
• using session charset: UTF-8 * current time: 2026-04-20 14:56:46 UTC
• checking for file ‘Colossus/DESCRIPTION’ ... OK
• checking extension type ... Package
• this is package ‘Colossus’ version ‘1.5’
• package encoding: UTF-8
• checking CRAN incoming feasibility ... [2s/3s] OK
• 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 serialization versions ... OK
• checking whether package ‘Colossus’ can be installed ... OK See the install log for details.
• used C compiler: ‘Debian clang version 21.1.8 (3+b1)’
• used C++ compiler: ‘Debian clang version 21.1.8 (3+b1)’
• checking C++ specification ... INFO   specified C++17
• checking package directory ... OK
• checking for future file timestamps ... OK
• checking ‘build’ 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 ... [2s/3s] OK
• checking whether the package can be loaded with stated dependencies ... [1s/2s] OK
• checking whether the package can be unloaded cleanly ... [1s/2s] OK
• checking whether the namespace can be loaded with stated dependencies ... [1s/2s] OK
• checking whether the namespace can be unloaded cleanly ... [2s/3s] OK
• checking loading without being on the library search path ... [2s/4s] OK
• checking whether startup messages can be suppressed ... [2s/3s] 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 ... [41s/65s] OK
• checking Rd files ... [1s/1s] 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 line endings in shell scripts ... OK
• checking line endings in C/C++/Fortran sources/headers ... OK
• checking line endings in Makefiles ... OK
• checking compilation flags in Makevars ... OK
• checking for GNU extensions in Makefiles ... OK
• checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
• checking use of PKG_*FLAGS in Makefiles ... OK
• checking use of SHLIB_OPENMP_*FLAGS in Makefiles ... OK
• checking pragmas in C/C++ headers and code ... OK
• checking compilation flags used ... OK
• checking compiled code ... OK
• checking installed files from ‘inst/doc’ ... OK
• checking files in ‘vignettes’ ... OK
• checking examples ... [5s/7s] OK
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [90s/114s] 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
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [80s/110s] OK
• checking PDF version of manual ... [6s/10s] OK
• checking HTML version of manual ... [5s/7s] OK
• checking for non-standard things in the check directory ... OK
• DONE

Status: 1 ERROR