various updates #178

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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/

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/

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Install dependencies

dependencies ‘Biostrings’, ‘MassSpecWavelet’, ‘orcutt’, ‘Biobase’, ‘marray’, ‘affy’, ‘limma’, ‘subselect’, ‘graph’, ‘Rgraphviz’, ‘rgeoda’, ‘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’, ‘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

Install dependencies