Change the URL checker to lychee

[cicdguy]

Instead of the urlchecker R package.
Also remove unnecessary exec permissions on files.

[github-actions]

Code Coverage Summary

Filename                           Stmts    Miss  Cover    Missing
-------------------------------  -------  ------  -------  --------------------------------
R/brier_score.R                      166       0  100.00%
R/DataJoint.R                         76       2  97.37%   264, 270
R/DataLongitudinal.R                 119       1  99.16%   244
R/DataSubject.R                       85       1  98.82%   142
R/DataSurvival.R                      98       0  100.00%
R/defaults.R                          10       6  40.00%   18-57, 84
R/generics.R                          31       4  87.10%   51, 395, 414, 449
R/Grid.R                              27       1  96.30%   170
R/GridEven.R                          32       0  100.00%
R/GridFixed.R                         30       0  100.00%
R/GridGrouped.R                       52       0  100.00%
R/GridManual.R                        23       3  86.96%   78-80
R/GridObserved.R                      20       0  100.00%
R/GridPopulation.R                    31       4  87.10%   61, 69-71
R/GridPrediction.R                    36       6  83.33%   83, 91-95
R/JointModel.R                       123       8  93.50%   141-143, 193, 197, 239, 285, 291
R/JointModelSamples.R                 59       0  100.00%
R/link_generics.R                     13       3  76.92%   59, 76, 91
R/Link.R                              62       4  93.55%   200-203
R/LinkComponent.R                     19       3  84.21%   88, 120-121
R/LongitudinalGSF.R                   82       0  100.00%
R/LongitudinalModel.R                 19       0  100.00%
R/LongitudinalQuantities.R            71       0  100.00%
R/LongitudinalRandomSlope.R           41       5  87.80%   93-97
R/LongitudinalSteinFojo.R             75       5  93.33%   143-147
R/Parameter.R                         14       0  100.00%
R/ParameterList.R                     42       1  97.62%   184
R/Prior.R                            236       8  96.61%   481, 577, 589-607
R/Promise.R                           25       0  100.00%
R/Quantities.R                        60       0  100.00%
R/QuantityGeneratorPopulation.R       22       0  100.00%
R/QuantityGeneratorPrediction.R       48       0  100.00%
R/QuantityGeneratorSubject.R          19       0  100.00%
R/settings.R                          12      12  0.00%    55-69
R/SimGroup.R                           5       0  100.00%
R/SimJointData.R                      72       1  98.61%   103
R/SimLongitudinal.R                    5       2  60.00%   22, 40
R/SimLongitudinalGSF.R                53       0  100.00%
R/SimLongitudinalRandomSlope.R        42       0  100.00%
R/SimLongitudinalSteinFojo.R          50       0  100.00%
R/SimSurvival.R                      104       0  100.00%
R/StanModel.R                         15       0  100.00%
R/StanModule.R                       176       6  96.59%   192-193, 235, 246, 383, 411
R/SurvivalExponential.R               10       0  100.00%
R/SurvivalLoglogistic.R               11       0  100.00%
R/SurvivalModel.R                     19       0  100.00%
R/SurvivalQuantities.R               170       1  99.41%   125
R/SurvivalWeibullPH.R                 11       0  100.00%
R/utilities.R                        143       1  99.30%   13
R/zzz.R                               28      25  10.71%   3, 8-12, 14-35, 47
TOTAL                               2792     113  95.95%

Diff against main

Filename      Stmts    Miss  Cover
----------  -------  ------  --------
TOTAL             0       0  +100.00%

Results for commit: 1a8268b

Minimum allowed coverage is 80%

♻️ This comment has been updated with latest results

[github-actions]

Unit Tests Summary

  1 files  132 suites   1m 42s ⏱️
124 tests  96 ✅ 27 💤 0 ❌ 1 🔥
891 runs  858 ✅ 32 💤 0 ❌ 1 🔥

For more details on these errors, see this check.

Results for commit 1a8268b.

♻️ This comment has been updated with latest results.

[github-actions]

Unit Test Performance Difference

Test Suite	$Status$	Time on main	$±Time$	$±Tests$	$±Skipped$	$±Failures$	$±Errors$
Grid	💀	$0.00$	$-0.00$	$-1$	$0$	$0$	$0$
JointModelSamples	💚	$5.46$	$-4.15$	$0$	$0$	$0$	$0$
compile	💚	$14.86$	$-11.00$	$0$	$0$	$0$	$0$
extract_quantities	💚	$16.45$	$-16.10$	$0$	$0$	$0$	$0$
model_multi_chain	💚	$70.83$	$-65.65$	$0$	$0$	$0$	$0$

Additional test case details

Test Suite	$Status$	Time on main	$±Time$	Test Case
DataSurvival	👶		$+21.50$	unnamed
Grid	💀	$0.00$	$-0.00$	GridFixed_bug_has_been_fixed
Grid	💀	$0.01$	$-0.01$	GridObservered_Constructs_correct_quantities
Grid	💀	$0.00$	$-0.00$	GridPopulation_doesn_t_work_with_SurvivalQuantities
Grid	💀	$0.01$	$-0.01$	GridPopulation_works_as_expected_for_GSF_models
Grid	💀	$0.01$	$-0.01$	GridPopulation_works_as_expected_for_Longitudinal_models
Grid	💀	$152.80$	$-152.80$	Grid_objects_work_with_QuantityGenerator_and_QuantityCollapser
Grid	💀	$0.01$	$-0.01$	coalesceGridTime_works_as_expected
Grid	💀	$0.01$	$-0.01$	subjects_to_list_works_as_expected
GridPrediction	💚	$150.53$	$-147.32$	GridPrediction_works_as_expected_for_Survival_models
JointModelSamples	💚	$5.46$	$-4.15$	print_works_as_expected_for_JointModelSamples
LinkComponent	💚	$2.93$	$-1.22$	all_link_files_pass_stan_s_syntax_checker
LongitudinalGSF	💚	$5.26$	$-4.99$	LongitudinalGSF_works_as_expected_with_default_arguments
LongitudinalQuantiles	💚	$30.09$	$-8.62$	Test_that_LongitudinalQuantities_works_as_expected
LongitudinalRandomSlope	💚	$56.89$	$-56.47$	Print_method_for_LongitudinalRandomSlope_works_as_expected
LongitudinalSteinFojo	💚	$375.02$	$-372.17$	LongitudinalSteinFojo_works_as_expected_with_default_arguments
SimSurvival	💚	$3.11$	$-1.19$	SimSurvivalExponential_creates_a_dataset_with_the_correct_parameter
SurvivalExponential	💚	$26.77$	$-21.48$	SurvivalExponential_can_recover_true_parameter_including_covariates_
SurvivalLoglogistic	💚	$46.34$	$-45.77$	sim_os_loglogistic_is_consistant_with_flexsurv
SurvivalQuantities	💚	$79.88$	$-71.75$	SurvivalQuantities_and_autoplot.SurvivalQuantities_works_as_expected
SurvivalWeibullPH	💚	$10.09$	$-2.52$	Print_method_for_SurvivalWeibullPH_works_as_expected
compile	💚	$14.86$	$-11.00$	compileStanModel_doesn_t_error_if_the_directory_doesn_t_exist
extract_quantities	💚	$16.45$	$-16.10$	extract_quantities_works_as_expected
model_multi_chain	💚	$70.83$	$-65.65$	Can_recover_known_distribution_parameters_from_random_slope_model_when_using_multiple_chains
stan_functions	💚	$68.32$	$-66.23$	GSF_SLD_function_works_as_expected

Results for commit 6529af5

♻️ This comment has been updated with latest results.