--- 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 job running on runner GitHub Actions 10 has exceeded the maximum execution time of 360 minutes.

FAILED

Compilation failed.

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/

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/

dependencies ‘graph’, ‘Biostrings’, ‘MassSpecWavelet’, ‘Biobase’, ‘marray’, ‘affy’, ‘limma’, ‘subselect’, ‘Rgraphviz’, ‘BiocParallel’, ‘BiocVersion’, ‘BiocStyle’, ‘rnaturalearthhires’, ‘dotwhisker’, ‘starsdata’, ‘snpStats’, ‘cmdstanr’, ‘spDataLarge’, ‘INLA’, ‘glmmADMB’, ‘bold’, ‘M3C’, ‘sylly.de’, ‘sylly.es’, ‘globaltest’, ‘ComplexHeatmap’, ‘cairoDevice’, ‘RGtk2’, ‘biomaRt’, ‘KEGGgraph’, ‘Rcampdf’, ‘tm.lexicon.GeneralInquirer’, ‘RandomFields’, ‘gurobi’, ‘rrelaxiv’, ‘taxidata’, ‘ExactData’, ‘rtracklayer’, ‘GenomicRanges’, ‘IRanges’, ‘S4Vectors’, ‘loe’, ‘genefilter’, ‘sva’, ‘RDCOMClient’, ‘RTCGA.rnaseq’, ‘rhdf5’, ‘Icens’, ‘mixOmics’, ‘aods3’ 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/

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’, ‘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’, ‘broom.helpers’, ‘ggpp’, ‘coneproj’, ‘glmmADMB’, ‘circlize’, ‘arules’, ‘ [... truncated]

dependencies ‘graph’, ‘Biostrings’, ‘MassSpecWavelet’, ‘Biobase’, ‘marray’, ‘affy’, ‘limma’, ‘subselect’, ‘Rgraphviz’, ‘BiocParallel’, ‘BiocVersion’, ‘BiocStyle’, ‘rnaturalearthhires’, ‘dotwhisker’, ‘starsdata’, ‘snpStats’, ‘cmdstanr’, ‘spDataLarge’, ‘INLA’, ‘glmmADMB’, ‘bold’, ‘M3C’, ‘sylly.de’, ‘sylly.es’, ‘globaltest’, ‘ComplexHeatmap’, ‘cairoDevice’, ‘RGtk2’, ‘biomaRt’, ‘KEGGgraph’, ‘Rcampdf’, ‘tm.lexicon.GeneralInquirer’, ‘RandomFields’, ‘gurobi’, ‘rrelaxiv’, ‘taxidata’, ‘ExactData’, ‘rtracklayer’, ‘GenomicRanges’, ‘IRanges’, ‘S4Vectors’, ‘loe’, ‘genefilter’, ‘sva’, ‘RDCOMClient’, ‘RTCGA.rnaseq’, ‘rhdf5’, ‘Icens’, ‘mixOmics’, ‘aods3’ 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

‘__builtin_memcpy’ writing 68 bytes into a region of size 50 overflows the destination [-Wstringop-overflow=]

no DISPLAY variable so Tk is not available

no DISPLAY variable so Tk is not available