408: skip problematic tests on R-devel non-standard clang linux systems

[danielinteractive]

closes https://github.com/openpharma/mmrm/issues/408 [skip vbump]

[danielinteractive]

Submitted to CRAN

[github-actions[bot]]

Code Coverage Summary

Filename                    Stmts    Miss  Cover    Missing
------------------------  -------  ------  -------  ----------------------------
R/between-within.R             59       0  100.00%
R/component.R                  67       0  100.00%
R/cov_struct.R                 97       1  98.97%   407
R/empirical.R                   7       0  100.00%
R/fit.R                       229       7  96.94%   186-189, 420, 481, 511
R/interop-car.R                70       2  97.14%   9, 48
R/interop-emmeans.R            39       0  100.00%
R/interop-parsnip.R            59       1  98.31%   12
R/kenwardroger.R               92       2  97.83%   41, 63
R/mmrm-methods.R              140       0  100.00%
R/residual.R                    8       8  0.00%    10-31
R/satterthwaite.R             116      12  89.66%   238-249
R/skipping.R                   30       0  100.00%
R/testing.R                    64       4  93.75%   29, 31, 80, 82
R/tidiers.R                    72       2  97.22%   46-47
R/tmb-methods.R               287       3  98.95%   277-278, 338
R/tmb.R                       281       0  100.00%
R/utils-formula.R              27       0  100.00%
R/utils-nse.R                  16       0  100.00%
R/utils.R                     184      12  93.48%   276-286, 456, 485
R/zzz.R                        70      24  65.71%   7-22, 55-60, 90, 118, 138
src/chol_cache.h               63       0  100.00%
src/covariance.h              101       1  99.01%   177
src/derivatives.h             126       0  100.00%
src/empirical.cpp              72       0  100.00%
src/exports.cpp                47       0  100.00%
src/jacobian.cpp               47       1  97.87%   54
src/kr_comp.cpp                56       0  100.00%
src/mmrm.cpp                   76       0  100.00%
src/predict.cpp                93       0  100.00%
src/test-chol_cache.cpp        58       5  91.38%   9, 18, 26, 55, 62
src/test-covariance.cpp       123       5  95.93%   9, 29, 40, 61, 72
src/test-derivatives.cpp      108       7  93.52%   44, 53, 62, 85, 94, 106, 124
src/test-utils.cpp            195       7  96.41%   9, 16, 24, 34, 44, 57, 119
src/testthat-helpers.h         15       5  66.67%   36-37, 41, 50, 53
src/utils.h                    84       0  100.00%
TOTAL                        3278     109  96.67%

Diff against main

Filename            Stmts    Miss  Cover
----------------  -------  ------  --------
R/mmrm-methods.R      +20       0  +100.00%
R/skipping.R          +30       0  +100.00%
TOTAL                 +50       0  +0.05%

Results for commit: 4ae99c2116c3db2d64b75edd267762fea0a35772

Minimum allowed coverage is 80%

:recycle: This comment has been updated with latest results

[github-actions[bot]]

Unit Tests Summary

    1 files     45 suites   23s :stopwatch:   493 tests   455 :white_check_mark: 38 :zzz: 0 :x: 1 896 runs  1 854 :white_check_mark: 42 :zzz: 0 :x:

Results for commit 4ae99c21.

:recycle: This comment has been updated with latest results.

[danielinteractive]

First step is ok:

package mmrm_0.3.8.tar.gz has been auto-processed. The auto-check found additional issues for the last version released on CRAN: clang18 https://www.stats.ox.ac.uk/pub/bdr/clang18/mmrm.out CRAN will have to check these additional issues manually.

[danielinteractive]

on clang18 we got the following problem report:

--- re-building ‘introduction.Rmd’ using rmarkdown

Quitting from lines 95-96 [mmrm_using_emp_start] (./subsections/_intro-customizations.Rmd)

Quitting from lines 95-96 [unnamed-chunk-3] (./subsections/_intro-customizations.Rmd) Error: processing vignette 'introduction.Rmd' failed with diagnostics: No optimizer led to a successful model fit. Please try to use a different covariance structure or other covariates. --- failed re-building ‘introduction.Rmd’

Therefore will skip this chunk conditionally under the same conditions.

[github-actions[bot]]

Unit Test Performance Difference

Test Suite	$Status$	Time on main	$±Time$	$±Tests$	$±Skipped$	$±Failures$	$±Errors$
skipping	👶		$+0.09$	$+20$	$0$	$0$	$0$

Additional test case details

| Test Suite | $Status$ | Time on `main` | $±Time$ | Test Case | |:-----|:----:|:----:|:----:|:-----| | mmrm-methods | 👶 | | $+0.09$ | confint_give_same_result_as_SAS_on_ar1 | | mmrm-methods | 👶 | | $+0.09$ | confint_give_same_result_as_SAS_on_unstructured | | mmrm-methods | 👶 | | $+0.07$ | confint_give_same_result_as_emmeans_if_no_interaction_term | | mmrm-methods | 👶 | | $+0.03$ | confint_works_for_different_parm_input | | mmrm-methods | 👶 | | $+0.04$ | confint_works_for_different_significance_levels | | skipping | 👶 | | $+0.01$ | is_linux_works_as_expected | | skipping | 👶 | | $+0.01$ | is_non_standard_clang_returns_FALSE_for_non_listed_Debian_versions | | skipping | 👶 | | $+0.01$ | is_non_standard_clang_returns_FALSE_for_non_listed_Fedora_versions | | skipping | 👶 | | $+0.01$ | is_non_standard_clang_returns_FALSE_for_other_Linux_distributions | | skipping | 👶 | | $+0.01$ | is_non_standard_clang_works_as_expected_for_Debian | | skipping | 👶 | | $+0.02$ | is_non_standard_clang_works_as_expected_for_Fedora | | skipping | 👶 | | $+0.00$ | is_r_devel_linux_clang_works_as_expected | | skipping | 👶 | | $+0.01$ | is_r_devel_works_as_expected | | skipping | 👶 | | $+0.01$ | is_using_clang_works_as_expected | | skipping | 👶 | | $+0.01$ | parse_clang_major_works_as_expected |

Results for commit 7292e949d0752c26fa856a2b919290a46a16668d

♻️ This comment has been updated with latest results.