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

object ‘palette.colors’ is not exported by 'namespace:grDevices'

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 operation was canceled.

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/

dependencies ‘graph’, ‘Biostrings’, ‘seqLogo’, ‘dblog’, ‘MassSpecWavelet’, ‘marray’, ‘affy’, ‘Biobase’, ‘limma’, ‘Rgraphviz’, ‘argon2’, ‘rnaturalearthhires’, ‘RandomFields’, ‘RandomFieldsUtils’, ‘starsdata’, ‘BiocVersion’, ‘ganalytics’, ‘cmdstanr’, ‘spDataLarge’, ‘glmmADMB’, ‘R2wd’, ‘M3C’, ‘hoa’, ‘sylly.de’, ‘sylly.es’, ‘INLA’, ‘globaltest’, ‘OpenMPController’, ‘lavaan.survey’, ‘ComplexHeatmap’, ‘snpStats’, ‘cairoDevice’, ‘RGtk2’, ‘sangerseqR’, ‘texPreview’, ‘biomaRt’, ‘KEGGgraph’, ‘Rcampdf’, ‘tm.lexicon.GeneralInquirer’, ‘taxidata’, ‘ExactData’, ‘corpus.JSS.papers’, ‘gurobi’, ‘rrelaxiv’, ‘RDCOMClient’, ‘RTCGA.rnaseq’, ‘rhdf5’, ‘mail’, ‘IRanges’, ‘extraTrees’, ‘genefilter’, ‘sva’, ‘Icens’ are not available

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/

unknown option ‘--no-bulid-vignettes’

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

dependencies ‘graph’, ‘phangorn’, ‘rjson’, ‘crew’, ‘Biobase’, ‘MassSpecWavelet’, ‘dblog’, ‘emmeans’, ‘ergm’, ‘gam’, ‘metafor’, ‘marray’, ‘affy’, ‘limma’, ‘VGAM’, ‘gsl’, ‘BiocVersion’, ‘MuMIn’, ‘Bergm’, ‘pbkrtest’, ‘fastICA’, ‘randomForest’, ‘Rgraphviz’, ‘rgeoda’, ‘argon2’, ‘rnaturalearthhires’, ‘RandomFields’, ‘RandomFieldsUtils’, ‘locfit’, ‘OpenStreetMap’, ‘starsdata’, ‘ganalytics’, ‘gdtools’, ‘psychotree’, ‘actuar’, ‘SGP’, ‘equatags’, ‘doconv’, ‘spDataLarge’, ‘phylolm’, ‘piecewiseSEM’, ‘lmeInfo’, ‘cmdstanr’, ‘glmmADMB’, ‘lattice’, ‘arules’, ‘metaBMA’, ‘metadat’, ‘mmrm’, ‘R2wd’, ‘sylly.de’, ‘sylly.es’, ‘INLA’, ‘tidySEM’, ‘globaltest’, ‘OpenMPController’, ‘lavaan.survey’, ‘semTools’, ‘ComplexHeatmap’, ‘haplo.stats’, ‘meta’, ‘FactoMineR’, ‘M [... truncated]

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/

dependencies ‘graph’, ‘Biostrings’, ‘seqLogo’, ‘dblog’, ‘MassSpecWavelet’, ‘marray’, ‘affy’, ‘Biobase’, ‘limma’, ‘Rgraphviz’, ‘argon2’, ‘rnaturalearthhires’, ‘RandomFields’, ‘RandomFieldsUtils’, ‘starsdata’, ‘BiocVersion’, ‘ganalytics’, ‘cmdstanr’, ‘spDataLarge’, ‘glmmADMB’, ‘R2wd’, ‘M3C’, ‘hoa’, ‘sylly.de’, ‘sylly.es’, ‘INLA’, ‘globaltest’, ‘OpenMPController’, ‘lavaan.survey’, ‘ComplexHeatmap’, ‘snpStats’, ‘cairoDevice’, ‘RGtk2’, ‘sangerseqR’, ‘texPreview’, ‘biomaRt’, ‘KEGGgraph’, ‘Rcampdf’, ‘tm.lexicon.GeneralInquirer’, ‘taxidata’, ‘ExactData’, ‘corpus.JSS.papers’, ‘gurobi’, ‘rrelaxiv’, ‘RDCOMClient’, ‘RTCGA.rnaseq’, ‘rhdf5’, ‘mail’, ‘IRanges’, ‘extraTrees’, ‘genefilter’, ‘sva’, ‘Icens’ are not available

no DISPLAY variable so Tk is not available

no DISPLAY variable so Tk is not available

no DISPLAY variable so Tk is not available

no DISPLAY variable so Tk is not available

no DISPLAY variable so Tk is not available

no DISPLAY variable so Tk is not available

no DISPLAY variable so Tk is not available

Fortran 2018 deleted feature: DO termination statement which is not END DO or CONTINUE with label 20 at (1)