CRAN Package Check Results for Package Colossus

Last updated on 2024-09-23 08:49:18 CEST.

Flavor	Version	T_install	T_check	T_total	Status
r-devel-linux-x86_64-debian-clang	1.1.3.1	229.71	147.61	377.32	OK
r-devel-linux-x86_64-debian-gcc	1.1.4.1	157.38	163.23	320.61	OK
r-devel-linux-x86_64-fedora-clang	1.1.4.1			724.15	ERROR
r-devel-linux-x86_64-fedora-gcc	1.1.4.1			893.29	OK
r-devel-windows-x86_64	1.1.4.1	148.00	215.00	363.00	OK
r-patched-linux-x86_64	1.1.3.1	211.84	206.02	417.86	OK
r-release-linux-x86_64	1.1.4.1	220.11	219.72	439.83	OK
r-release-macos-arm64	1.1.4.1			166.00	NOTE
r-release-macos-x86_64	1.1.3.1			315.00	NOTE
r-release-windows-x86_64	1.1.4.1	139.00	218.00	357.00	OK
r-oldrel-macos-arm64	1.1.4.1			205.00	NOTE
r-oldrel-macos-x86_64	1.1.3.1			459.00	NOTE
r-oldrel-windows-x86_64	1.1.4.1	136.00	243.00	379.00	OK

Check Details

Version: 1.1.4.1
Check: tests
Result: ERROR Running ‘spelling.R’ Running ‘testthat.R’ [214s/363s] 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 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 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 5 | WARN 0 | SKIP 0 | PASS 1035 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test-Cox_Regression.R:211:5'): Coxph loglin_plin_A ──────────────── e$beta_0 (`actual`) not equal to c(0.11, 1.01) (`expected`). `actual`: 0.03 0.63 `expected`: 0.11 1.01 ── Failure ('test-Cox_Regression.R:271:5'): Coxph loglin_M Strata ────────────── e$beta_0 (`actual`) not equal to c(-0.106) (`expected`). `actual`: -0.10 `expected`: -0.11 ── Failure ('test-Cox_Regression.R:290:5'): Coxph loglin_M Single ────────────── e$AIC (`actual`) not equal to 1056.299 (`expected`). `actual`: 2109 `expected`: 1056 ── Failure ('test-Cox_Regression.R:432:5'): Coxph censoring weight ───────────── e0$LogLik - e1$LogLik (`actual`) not equal to -2.909427 (`expected`). `actual`: -126 `expected`: -3 ── Failure ('test-Poisson_Regression.R:164:5'): Pois loglin_M Strata ─────────── e$beta_0 (`actual`) not equal to c(0.05476188) (`expected`). `actual`: 0.3 `expected`: 0.1 [ FAIL 5 | WARN 0 | SKIP 0 | PASS 1035 ] Error: Test failures Execution halted Flavor: r-devel-linux-x86_64-fedora-clang

Version: 1.1.4.1
Check: installed package size
Result: NOTE installed size is 67.2Mb sub-directories of 1Mb or more: libs 66.1Mb Flavors: r-release-macos-arm64, r-oldrel-macos-arm64

Version: 1.1.3.1
Check: installed package size
Result: NOTE installed size is 83.0Mb sub-directories of 1Mb or more: libs 82.1Mb Flavors: r-release-macos-x86_64, r-oldrel-macos-x86_64