CRAN Package Check Results for Package Colossus

Last updated on 2024-09-18 12:48:19 CEST.

Flavor	Version	T_install	T_check	T_total	Status
r-devel-linux-x86_64-debian-clang	1.1.3.1	214.78	150.31	365.09	OK
r-devel-linux-x86_64-debian-gcc	1.1.3.1	156.66	175.99	332.65	OK
r-devel-linux-x86_64-fedora-clang	1.1.3.1			692.06	ERROR
r-devel-linux-x86_64-fedora-gcc	1.1.3.1			786.86	OK
r-devel-windows-x86_64	1.1.3.1	141.00	194.00	335.00	OK
r-patched-linux-x86_64	1.1.3.1	219.94	215.23	435.17	OK
r-release-linux-x86_64	1.1.3.1	219.07	224.10	443.17	OK
r-release-macos-arm64	1.1.3.1			172.00	NOTE
r-release-macos-x86_64	1.1.3.1			315.00	NOTE
r-release-windows-x86_64	1.1.3	163.00	211.00	374.00	OK
r-oldrel-macos-arm64	1.1.3.1			202.00	NOTE
r-oldrel-macos-x86_64	1.1.3.1			459.00	NOTE
r-oldrel-windows-x86_64	1.1.3.1	212.00	244.00	456.00	OK

Check Details

Version: 1.1.3.1
Check: tests
Result: ERROR Running ‘spelling.R’ Running ‘testthat.R’ [214s/194s] 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") Error: no events Error: Plot type not given Error: Stratification Column not in dataframe Error: Stratification Column not given Error: dose column not given Error: dose column not given Note: Starting Plot Function Note: Getting Plot Info Note: 2 risk groups Error: ID column is not in the dataframe Note: Starting Plot Function Note: Getting Plot Info Note: 2 risk groups Error: ID column not given Note: 3 risk groups Warning: element 1 with column name d was set constant Error: Atleast one parameter must be free Note: 3 risk groups Saving 7 x 7 in image Saving 7 x 7 in image Saving 7 x 7 in image Saving 7 x 7 in image Note: 3 risk groups Note: 2 strata used Note: 2 strata used Note: 3 risk groups Saving 7 x 7 in image Note: 3 risk groups Saving 7 x 7 in image Note: 86 risk groups Note: 86 risk groups Saving 7 x 7 in image Saving 7 x 7 in image Saving 7 x 7 in image Saving 7 x 7 in image Note: 2 risk groups Saving 7 x 7 in image Saving 7 x 7 in image Note: Starting Plot Function Note: Getting Plot Info Note: 3 risk groups Note: 3 risk groups Note: starting ph_plot Note: nonStratified survival curve calculation Note: writing survival data Note: Plotting Survival Curves Saving 7 x 7 in image Saving 7 x 7 in image Saving 7 x 7 in image Saving 7 x 7 in image Note: Plotting Kaplan-Meier Curve Saving 7 x 7 in image Saving 7 x 7 in image Saving 7 x 7 in image Saving 7 x 7 in image Error: Cores Requested: 124 , Cores Available: 2 Error: e not in data.table Error: e not in data.table Error: Iteration: a?+?b?+c has incorrect length of 4 but should be 3. Error: Incorrect operation of ++ Error: Terms used: 2 , Terms with gmix types available: 1 Error: Model formula FAILING_CHOICE not in acceptable list Error: Model formula MA not in acceptable list Error: Model formula EA not in acceptable list Error: Interpolation method not recognized: badbad Error: a0 arguement was negative Error: a0 arguement was not a number Error: a0 arguement was not a number Error: a0 arguement was negative Error: a0 arguement was not a number Error: a0 arguement was not a number Error: a0 arguement was not a number Error: goal is too low Error: a0 arguement was negative Error: e missing from column names Error: The missing-value replacement is also NA Warning: Parameters used: 4, Covariates used: 5, Remaining filled with 0.01 Error: Atleast one parameter must be free Error: Parameters used: 6, Covariates used: 5 Error: Terms used: 4, Covariates used: 5 Error: Terms used: 6, Covariates used: 5 Error: Term types used: 4, Covariates used: 5 Error: Term types used: 6, Covariates used: 5 Error: lin_int missing Error: step_int missing Error: loglin_top missing Error: lin_quad_int missing Error: lin_exp_int missing Error: lin_exp_exp_slope missing Error: step_slope missing Error: lin_slope missing Error: lin_quad_slope missing Error: lin_exp_slope missing Error: lin_exp_int missing Error: Parameters used in first option: 5, Parameters used in different option: 4, please fix parameter length Warning: Parameters used: 4, Covariates used: 5, Remaining filled with 0.01 Error: Parameters used: 6, Covariates used: 5 Error: Terms used: 4, Covariates used: 5 Error: Terms used: 6, Covariates used: 5 Error: Term types used: 4, Covariates used: 5 Error: Term types used: 6, Covariates used: 5 Error: verbosity arguement not valid Error: verbosity arguement not valid Error: verbosity arguement not valid Error: keep_constant expects 0/1 values, minimum value was -1 Error: keep_constant expects 0/1 values, maximum value was 10 Error: keep_constant expects 0/1 values, atleast one value was noninteger Warning: term_n expects nonnegative integer values and a minimum of 0, minimum value was -1. Minimum value set to 0, others shifted by 1 Error: term_n expects integer values, atleast one value was noninteger Error: term_n expects no missing integer values. Term numbers range from 0 to 3 but term_n has 3 unique values instead of 4 Warning: term_n expects nonnegative integer values and a minimum of 0, minimum value was -1. Minimum value set to 0, others shifted by 1 Error: Missing tform items: missing fake Warning: term_n expects nonnegative integer values and a minimum of 0, minimum value was -1. Minimum value set to 0, others shifted by 1 Error: Missing tform items: missing fake missing bad Error: Default Parameters used: 7, Covariates used: 4 Error: Terms used: 1, Covariates used: 4 Error: Terms used: 8, Covariates used: 4 Error: Term types used: 1, Covariates used: 4 Error: Term types used: 5, Covariates used: 4 Error: Atleast one parameter must be free Error: no events Warning: rmin and rmax lists not equal size, defaulting to lin and loglin min/max values Warning: rmin and rmax lists not equal size, defaulting to lin and loglin min/max values Error: tform not implemented bad_bad Error: der_iden should be within 0:(length(tform)-1) Error: der_iden should be within 0:(length(tform)-1) Error: Constraint matrix has incorrect number of columns Error: Constraint rows and constant lengths do not match Error: verbosity arguement not valid Warning: model covariate order changed Error: Atleast one parameter must be free Warning: model covariate order changed Error: no events Warning: model covariate order changed Warning: model covariate order changed Error: guesses: 100 , iterations per guess: c(1, 1) Warning: rmin and rmax lists not equal size, defaulting to lin and loglin min/max values Warning: rmin and rmax lists not equal size, defaulting to lin and loglin min/max values Warning: term_n expects nonnegative integer values and a minimum of 0, minimum value was 1. Minimum value set to 0, others shifted by -1 Warning: rmin and rmax lists not equal size, defaulting to lin and loglin min/max values Warning: term_n expects nonnegative integer values and a minimum of 0, minimum value was 1. Minimum value set to 0, others shifted by -1 Error: Atleast one parameter must be free Warning: rmin and rmax lists not equal size, defaulting to lin and loglin min/max values Error: guesses_control and model_control have different strata options Warning: rmin and rmax lists not equal size, defaulting to lin and loglin min/max values Error: Atleast one parameter must be free Warning: rmin and rmax lists not equal size, defaulting to lin and loglin min/max values Note: 2 risk groups Saving 7 x 7 in image Saving 7 x 7 in image Note: 908 risk groups Saving 7 x 7 in image Error: Atleast one parameter must be free Error: no events Note: 3 risk groups Saving 7 x 7 in image Warning: model covariate order changed Note: 26 risk groups Error: Atleast one parameter must be free Warning: model covariate order changed Warning: model covariate order changed Note: 26 risk groups Note: Initial starts: 1 , Number of iterations provided: 4 . Colossus requires one more iteration counts than number of guesses (for best guess) Warning: model covariate order changed Note: 26 risk groups Note: Initial starts: 3 , Number of iterations provided: 2 . Colossus requires one more iteration counts than number of guesses (for best guess) Warning: model covariate order changed Note: 26 risk groups Warning: model covariate order changed Note: 26 risk groups Warning: model covariate order changed Note: 26 risk groups Error: Invalid risk Warning: model covariate order changed Error: Atleast one parameter must be free Warning: model covariate order changed Error: no events Warning: model covariate order changed Note: Initial starts: 1 , Number of iterations provided: 4 . Colossus requires one more iteration counts than number of guesses (for best guess) Warning: model covariate order changed Note: Initial starts: 3 , Number of iterations provided: 2 . Colossus requires one more iteration counts than number of guesses (for best guess) Warning: model covariate order changed Error: guesses: 50 , iterations per guess: c(1, 1) Warning: model covariate order changed Warning: model covariate order changed Warning: model covariate order changed Error: Invalid risk Error: Atleast one parameter must be free Error: Atleast one parameter must be free Warning: model covariate order changed Note: 2 risk groups Saving 7 x 7 in image Saving 7 x 7 in image Error: no events Error: Atleast one parameter must be free Warning: rmin/rmax not equal size, lin/loglin min/max used Warning: rmin and rmax lists not equal size, defaulting to lin and loglin min/max values Note: 86 risk groups Warning: rmin and rmax lists not equal size, defaulting to lin and loglin min/max values Note: 86 risk groups Error: guesses_control and model_control have different strata options Note: 2 strata used Warning: rmin and rmax lists not equal size, defaulting to lin and loglin min/max values Note: 2 strata used Note: 86 risk groups Error: Atleast one parameter must be free Error: no events Error: Default Parameters used: 4, Covariates used: 6 Warning: rmin and rmax lists not equal size, defaulting to lin and loglin min/max values Error: tform not implemented Not Warning: rmin and rmax lists not equal size, defaulting to lin and loglin min/max values Error: verbosity arguement not valid Error: verbosity arguement not valid Error: a0 arguement was not a number Error: a0 arguement was not a number Error: a0 arguement was not a number Error: item e1 in name_list has 1 items, but same item in term_n_list has 6 items. Omit entry in term_n_list to set to default of term 0 or add missing values Error: item e1 in name_list has 1 items, but same item in tform_list has 6 items. Omit entry in tform_list to set to default of 'loglin' or add missing values Error: item e1 in name_list has 1 items, but same item in keep_constant_list has 6 items. Omit entry in tform_list to set to default of 0 or add missing values Error: item e1 in name_list has 1 items, but same item in a_n_list has 6 items. Omit entry in a_n_list to set to default of 0 or add missing values Saving 7 x 7 in image Note: 5 strata used Note: 26 risk groups Note: 5 strata used Note: 26 risk groups Note: 5 strata used Note: 26 risk groups Note: 5 strata used Note: 26 risk groups Note: 5 strata used Note: 26 risk groups Note: 5 strata used Note: 26 risk groups Note: 5 strata used Note: 26 risk groups Note: 5 strata used Note: 26 risk groups Note: 5 strata used Note: 26 risk groups Note: 5 strata used Note: 26 risk groups Note: 5 strata used Note: 26 risk groups Note: 5 strata used Note: 26 risk groups Note: 5 strata used Note: 26 risk groups Note: 5 strata used Note: 26 risk groups Note: 5 strata used Note: 26 risk groups Note: 5 strata used Note: 26 risk groups Note: 5 strata used Note: 26 risk groups Note: 5 strata used Note: 26 risk groups Note: 5 strata used Note: 26 risk groups Note: 5 strata used Note: 26 risk groups Note: 5 strata used Note: 26 risk groups Note: 5 strata used Note: 26 risk groups Note: 5 strata used Note: 26 risk groups Note: 5 strata used Note: 26 risk groups Note: 5 strata used Note: 26 risk groups Note: 5 strata used Note: 26 risk groups Note: 5 strata used Note: 26 risk groups Note: 5 strata used Note: 26 risk groups Note: 5 strata used Note: 26 risk groups Note: 5 strata used Note: 26 risk groups Note: 5 strata used Note: 26 risk groups Note: 5 strata used Note: 26 risk groups Note: 26 risk groups Note: 26 risk groups Note: 26 risk groups Note: 26 risk groups Note: 26 risk groups Note: 26 risk groups Note: 26 risk groups Note: 26 risk groups Note: 26 risk groups Note: 26 risk groups Note: 26 risk groups Note: 26 risk groups Note: 26 risk groups Note: 26 risk groups Note: 26 risk groups Note: 26 risk groups Note: 26 risk groups Note: 26 risk groups Note: 26 risk groups Note: 26 risk groups Note: 26 risk groups Note: 26 risk groups Note: 26 risk groups Note: 26 risk groups Note: 26 risk groups Note: 26 risk groups Note: 26 risk groups Note: 26 risk groups Note: 26 risk groups Note: 26 risk groups Note: 26 risk groups Note: 26 risk groups Note: 26 risk groups Error: Invalid model Note: 26 risk groups Error: Invalid model Note: 26 risk groups Error: Invalid model Note: 26 risk groups Error: Invalid model Error: Invalid model Error: Invalid model Note: 1 risk groups Note: 1 risk groups Note: 99 risk groups Note: 99 risk groups Note: 2 strata used Note: 99 risk groups Note: 2 strata used Note: 99 risk groups [1] "starting" Note: 99 risk groups Error: 2 column indexes provided, but 1 rows of realizations columns provided Note: 99 risk groups Error: Atleast one realization column provided was not in the data.table Note: 99 risk groups Error: bad missing from column names Error: no events Note: 99 risk groups non-derivative model calculation is not compatable with multi-realization method Error: Invalid model Note: 99 risk groups null model is not compatable with multi-realization method Error: Invalid model Note: 114 risk groups Note: 114 risk groups Note: 114 risk groups Note: 114 risk groups Note: 114 risk groups Note: 114 risk groups Note: 114 risk groups Note: 114 risk groups Note: 114 risk groups Note: 2 strata used Note: 114 risk groups Note: 2 strata used Note: 114 risk groups Note: 2 strata used Note: 114 risk groups Note: 2 strata used Note: 114 risk groups Note: 2 strata used Note: 114 risk groups Note: 2 strata used Note: 114 risk groups Note: 2 strata used Note: 114 risk groups Note: 2 strata used Note: 114 risk groups Note: 2 strata used Note: 114 risk groups Note: 901 risk groups Saving 7 x 7 in image Note: 5 strata used Note: 26 risk groups THE ERROR IS AT INDEX 1 Note: 5 strata used Note: 26 risk groups Note: 5 strata used Note: 26 risk groups Note: 5 strata used Note: 26 risk groups Note: 5 strata used Note: 26 risk groups Note: 5 strata used Note: 26 risk groups THE ERROR IS AT INDEX 6 Note: 5 strata used Note: 26 risk groups THE ERROR IS AT INDEX 7 Note: 5 strata used Note: 26 risk groups Note: 5 strata used Note: 26 risk groups Note: 5 strata used Note: 26 risk groups Note: 5 strata used Note: 26 risk groups Note: 5 strata used Note: 26 risk groups Note: 5 strata used Note: 26 risk groups THE ERROR IS AT INDEX 13 Note: 5 strata used Note: 26 risk groups Note: 5 strata used Note: 26 risk groups Note: 5 strata used Note: 26 risk groups Note: 26 risk groups Note: 26 risk groups Note: 26 risk groups Note: 26 risk groups Note: 26 risk groups THE ERROR IS AT INDEX 21 Note: 26 risk groups Note: 26 risk groups Note: 26 risk groups THE ERROR IS AT INDEX 24 Note: 26 risk groups THE ERROR IS AT INDEX 25 Note: 26 risk groups Note: 26 risk groups Note: 26 risk groups Note: 26 risk groups THE ERROR IS AT INDEX 29 Note: 26 risk groups Note: 26 risk groups Note: 26 risk groups Warning: model covariate order changed Warning: model covariate order changed Warning: model covariate order changed Warning: model covariate order changed Warning: model covariate order changed Warning: model covariate order changed Warning: model covariate order changed Warning: model covariate order changed [ FAIL 29 | WARN 0 | SKIP 0 | PASS 1541 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test-Cox_Regression.R:432:5'): Coxph censoring weight ───────────── e0$LogLik - e1$LogLik (`actual`) not equal to -2.909427 (`expected`). `actual`: -126 `expected`: -3 ── Failure ('test-logbound.R:214:9'): Coxph EPICURE validated answers, loglin manual ── a[1] (`actual`) not equal to v_lower[alpha_i] (`expected`). `actual`: -2 `expected`: 5 ── Failure ('test-logbound.R:215:9'): Coxph EPICURE validated answers, loglin manual ── a[2] (`actual`) not equal to v_upper[alpha_i] (`expected`). `actual`: 8 `expected`: 5 ── Failure ('test-logbound.R:257:8'): Coxph, lin both ────────────────────────── a[1] (`actual`) not equal to v_lower[alpha_i] (`expected`). `actual`: -13 `expected`: 5 ── Failure ('test-logbound.R:258:8'): Coxph, lin both ────────────────────────── a[2] (`actual`) not equal to v_upper[alpha_i] (`expected`). `actual`: 40 `expected`: 5 ── Failure ('test-multidose.R:52:13'): Coxph multidose ───────────────────────── LL_comp_1[k] (`actual`) not equal to val[1] (`expected`). `actual`: -450.9 `expected`: -451.7 ── Failure ('test-multidose.R:53:13'): Coxph multidose ───────────────────────── LL_comp_2[k] (`actual`) not equal to val[2] (`expected`). `actual`: -449.61 `expected`: -449.71 ── Failure ('test-multidose.R:54:13'): Coxph multidose ───────────────────────── LL_comp_3[k] (`actual`) not equal to val[3] (`expected`). `actual`: -451.8 `expected`: -451.6 ── Failure ('test-multidose.R:53:13'): Coxph multidose ───────────────────────── LL_comp_2[k] (`actual`) not equal to val[2] (`expected`). `actual`: -450 `expected`: -899 ── Failure ('test-multidose.R:54:13'): Coxph multidose ───────────────────────── LL_comp_3[k] (`actual`) not equal to val[3] (`expected`). `actual`: -452 `expected`: -904 ── Failure ('test-multidose.R:53:13'): Coxph multidose ───────────────────────── LL_comp_2[k] (`actual`) not equal to val[2] (`expected`). `actual`: -381.8 `expected`: -382.2 ── Failure ('test-multidose.R:52:13'): Coxph multidose ───────────────────────── LL_comp_1[k] (`actual`) not equal to val[1] (`expected`). `actual`: -383 `expected`: -766 ── Failure ('test-multidose.R:53:13'): Coxph multidose ───────────────────────── LL_comp_2[k] (`actual`) not equal to val[2] (`expected`). `actual`: -382 `expected`: -764 ── Failure ('test-multidose.R:54:13'): Coxph multidose ───────────────────────── LL_comp_3[k] (`actual`) not equal to val[3] (`expected`). `actual`: -382.9 `expected`: -383.2 ── Failure ('test-omnibus.R:30:17'): Coxph basic_single_null match ───────────── e0$LogLik (`actual`) not equal to e1$LogLik (`expected`). `actual`: -526 `expected`: -1052 ── Failure ('test-omnibus.R:30:17'): Coxph basic_single_null match ───────────── e0$LogLik (`actual`) not equal to e1$LogLik (`expected`). `actual`: -526 `expected`: -1052 ── Failure ('test-omnibus.R:44:17'): Coxph basic_single_null match ───────────── e0$LogLik (`actual`) not equal to e1$LogLik (`expected`). `actual`: -447 `expected`: -895 ── Failure ('test-omnibus.R:106:21'): Coxph strata_basic_single_CR ───────────── e$LogLik (`actual`) not equal to LL_comp[j_iterate] (`expected`). `actual`: -162 `expected`: -81 ── Failure ('test-omnibus.R:115:21'): Coxph strata_basic_single_CR ───────────── e$LogLik (`actual`) not equal to LL_comp[j_iterate] (`expected`). `actual`: -137 `expected`: -69 ── Failure ('test-omnibus.R:106:21'): Coxph strata_basic_single_CR ───────────── e$LogLik (`actual`) not equal to LL_comp[j_iterate] (`expected`). `actual`: -151 `expected`: -75 ── Failure ('test-omnibus.R:115:21'): Coxph strata_basic_single_CR ───────────── e$LogLik (`actual`) not equal to LL_comp[j_iterate] (`expected`). `actual`: -77 `expected`: -75 ── Failure ('test-omnibus.R:106:21'): Coxph strata_basic_single_CR ───────────── e$LogLik (`actual`) not equal to LL_comp[j_iterate] (`expected`). `actual`: -139 `expected`: -69 ── Failure ('test-omnibus.R:106:21'): Coxph strata_basic_single_CR ───────────── e$LogLik (`actual`) not equal to LL_comp[j_iterate] (`expected`). `actual`: -219 `expected`: -110 ── Failure ('test-omnibus.R:115:21'): Coxph strata_basic_single_CR ───────────── e$LogLik (`actual`) not equal to LL_comp[j_iterate] (`expected`). `actual`: -234 `expected`: -117 ── Failure ('test-omnibus.R:106:21'): Coxph strata_basic_single_CR ───────────── e$LogLik (`actual`) not equal to LL_comp[j_iterate] (`expected`). `actual`: -246 `expected`: -123 ── Failure ('test-omnibus.R:106:21'): Coxph strata_basic_single_CR ───────────── e$LogLik (`actual`) not equal to LL_comp[j_iterate] (`expected`). `actual`: -219 `expected`: -110 ── Failure ('test-omnibus.R:253:13'): Pois strata_single expanded ────────────── e$LogLik (`actual`) not equal to LL_comp[j_iterate] (`expected`). `actual`: -458 `expected`: -467 ── Failure ('test-omnibus.R:519:5'): check deviation calc ────────────────────── `devs` (`actual`) not equal to c(0.6091269, 0.5356671, 0.7385757, 0.9448081) (`expected`). `actual`: 0.4307 0.3788 0.7386 0.6681 `expected`: 0.6091 0.5357 0.7386 0.9448 ── Failure ('test-omnibus.R:549:9'): check Linear Constraints ────────────────── e$beta_0 (`actual`) not equal to c(0.357333, 0.357333) (`expected`). `actual`: -0.0 -0.3 `expected`: 0.4 0.4 [ FAIL 29 | WARN 0 | SKIP 0 | PASS 1541 ] Error: Test failures Execution halted Flavor: r-devel-linux-x86_64-fedora-clang

Version: 1.1.3.1
Check: installed package size
Result: NOTE installed size is 67.1Mb sub-directories of 1Mb or more: libs 66.1Mb Flavors: r-release-macos-arm64, r-release-macos-x86_64, r-oldrel-macos-arm64, r-oldrel-macos-x86_64