--- re-building ‘DrawingPhylogenies.Rnw’ using Sweave

processing vignette 'RandomTopologies.Rnw' failed with diagnostics:

there is no package called ‘phangorn’

Vignette re-building failed.

Build process failed

Process completed with exit code 1.

package ‘Matrix’ 1.2.18 was found, but >= 1.3 is required by ‘MatrixExtra’

package or namespace load failed for ‘lbfgsb3c’ in dyn.load(file, DLLpath = DLLpath, ...):

loading failed

package ‘rainbow’ required by ‘fds’ could not be found

package or namespace load failed for ‘dynlm’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):

package ‘dynlm’ could not be loaded

The following actions uses node12 which is deprecated and will be forced to run on node16: actions/checkout@v2, actions/cache@v2. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/

The following actions use a deprecated Node.js version and will be forced to run on node20: actions/checkout@v2, actions/cache@v2. For more info: https://github.blog/changelog/2024-03-07-github-actions-all-actions-will-run-on-node20-instead-of-node16-by-default/

unknown option ‘--no-bulid-vignettes’

No files were found with the provided path: check. No artifacts will be uploaded.

dependencies ‘pkgdown’, ‘graph’, ‘downlit’, ‘arrow’, ‘Hmisc’, ‘profvis’, ‘phangorn’, ‘rjson’, ‘rhub’, ‘XML’, ‘crew’, ‘Biobase’, ‘httr2’, ‘emmeans’, ‘ergm’, ‘gam’, ‘metafor’, ‘survey’, ‘marray’, ‘affy’, ‘limma’, ‘gsl’, ‘BiocParallel’, ‘BiocVersion’, ‘BiocStyle’, ‘rms’, ‘MuMIn’, ‘RODBC’, ‘Matrix’, ‘Bergm’, ‘pbkrtest’, ‘rio’, ‘fastICA’, ‘randomForest’, ‘subselect’, ‘estimability’, ‘FNN’, ‘VGAM’, ‘Rgraphviz’, ‘rgeoda’, ‘rnaturalearthhires’, ‘randomForestSRC’, ‘dotwhisker’, ‘rasterVis’, ‘locfit’, ‘OpenStreetMap’, ‘starsdata’, ‘gdtools’, ‘psychotree’, ‘keras3’, ‘unmarked’, ‘subplex’, ‘actuar’, ‘SGP’, ‘doconv’, ‘equatags’, ‘spDataLarge’, ‘phylolm’, ‘piecewiseSEM’, ‘lmeInfo’, ‘ggstats’, ‘broom.helpers’, ‘ggpp’, ‘coneproj’, ‘glmmADMB’, ‘ [... truncated]