--- 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 ‘marginaleffects’:

loading failed

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 ‘ggplot2’ in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):

package ‘ggplot2’ could not be loaded

package or namespace load failed for ‘ggplot2’ in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):

package ‘ggplot2’ could not be loaded

FAILED

Compilation failed.

No space left on device : '/home/runner/runners/2.321.0/_diag/blocks/0e74f279-68d2-4ecb-8812-7503f303fcd8_d0bbf2ed-d4bd-5606-fa6e-8bad841fe3b2.91'

Your workflow is using a version of actions/cache that is scheduled for deprecation, actions/cache@v2. Please update your workflow to use the latest version of actions/cache to avoid interruptions. Learn more: https://github.blog/changelog/2024-09-16-notice-of-upcoming-deprecations-and-changes-in-github-actions-services/

Your workflow is using a version of actions/cache that is scheduled for deprecation, actions/cache@v2. Please update your workflow to use the latest version of actions/cache to avoid interruptions. Learn more: https://github.blog/changelog/2024-09-16-notice-of-upcoming-deprecations-and-changes-in-github-actions-services/

Your workflow is using a version of actions/cache that is scheduled for deprecation, actions/cache@v2. Please update your workflow to use the latest version of actions/cache to avoid interruptions. Learn more: https://github.blog/changelog/2024-09-16-notice-of-upcoming-deprecations-and-changes-in-github-actions-services/

dependencies ‘Biostrings’, ‘MassSpecWavelet’, ‘orcutt’, ‘Biobase’, ‘marray’, ‘affy’, ‘limma’, ‘graph’, ‘Rgraphviz’, ‘BiocParallel’, ‘BiocVersion’, ‘BiocStyle’, ‘rnaturalearthhires’, ‘starsdata’, ‘snpStats’, ‘taxize’, ‘cmdstanr’, ‘Vdgraph’, ‘spDataLarge’, ‘INLA’, ‘glmmADMB’, ‘M3C’, ‘iwmm’, ‘sylly.de’, ‘sylly.es’, ‘globaltest’, ‘ComplexHeatmap’, ‘mvPot’, ‘cairoDevice’, ‘RGtk2’, ‘gurobi’, ‘rrelaxiv’, ‘pkgmaker’, ‘biomaRt’, ‘KEGGgraph’, ‘Rcampdf’, ‘tm.lexicon.GeneralInquirer’, ‘RandomFields’, ‘taxidata’, ‘ExactData’, ‘rtracklayer’, ‘GenomicRanges’, ‘IRanges’, ‘S4Vectors’, ‘loe’, ‘genefilter’, ‘sva’, ‘RDCOMClient’, ‘RTCGA.rnaseq’, ‘Icens’, ‘mlr3proba’, ‘rhdf5’, ‘mixOmics’ are not available

unknown option ‘--no-bulid-vignettes’

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

dependencies ‘waldo’, ‘pkgdown’, ‘cpp11’, ‘vdiffr’, ‘downlit’, ‘arrow’, ‘phangorn’, ‘rjson’, ‘Hmisc’, ‘rhub’, ‘XML’, ‘crew’, ‘gtable’, ‘profvis’, ‘Biobase’, ‘httr2’, ‘emmeans’, ‘ergm’, ‘gam’, ‘metafor’, ‘orcutt’, ‘survey’, ‘DPQ’, ‘gsl’, ‘BiocParallel’, ‘nanoparquet’, ‘marray’, ‘affy’, ‘limma’, ‘BiocVersion’, ‘BiocStyle’, ‘rms’, ‘MuMIn’, ‘RODBC’, ‘Matrix’, ‘Bergm’, ‘pbkrtest’, ‘rio’, ‘fastICA’, ‘randomForest’, ‘estimability’, ‘FNN’, ‘VGAM’, ‘graph’, ‘Rgraphviz’, ‘slider’, ‘spam’, ‘rasterVis’, ‘locfit’, ‘OpenStreetMap’, ‘starsdata’, ‘gdtools’, ‘psychotree’, ‘keras3’, ‘rnaturalearthhires’, ‘randomForestSRC’, ‘unmarked’, ‘subplex’, ‘actuar’, ‘SGP’, ‘taxize’, ‘logger’, ‘doconv’, ‘equatags’, ‘spDataLarge’, ‘piecewiseSEM’, ‘lmeInfo [... truncated]

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

dependencies ‘Biostrings’, ‘MassSpecWavelet’, ‘orcutt’, ‘Biobase’, ‘marray’, ‘affy’, ‘limma’, ‘graph’, ‘Rgraphviz’, ‘BiocParallel’, ‘BiocVersion’, ‘BiocStyle’, ‘rnaturalearthhires’, ‘starsdata’, ‘snpStats’, ‘taxize’, ‘cmdstanr’, ‘Vdgraph’, ‘spDataLarge’, ‘INLA’, ‘glmmADMB’, ‘M3C’, ‘iwmm’, ‘sylly.de’, ‘sylly.es’, ‘globaltest’, ‘ComplexHeatmap’, ‘mvPot’, ‘cairoDevice’, ‘RGtk2’, ‘gurobi’, ‘rrelaxiv’, ‘pkgmaker’, ‘biomaRt’, ‘KEGGgraph’, ‘Rcampdf’, ‘tm.lexicon.GeneralInquirer’, ‘RandomFields’, ‘taxidata’, ‘ExactData’, ‘rtracklayer’, ‘GenomicRanges’, ‘IRanges’, ‘S4Vectors’, ‘loe’, ‘genefilter’, ‘sva’, ‘RDCOMClient’, ‘RTCGA.rnaseq’, ‘Icens’, ‘mlr3proba’, ‘rhdf5’, ‘mixOmics’ 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