{ "_id": "6a22b7cf0ef520ea2f58ffd8", "Package": "phyloatlas", "Type": "Package", "Title": "Access to the 'Phylo-Species Atlas' of Empirical Phylogenies", "Version": "0.1.0", "Authors@R": "person(given = \"Francisco\",\nfamily = \"Richter\",\nemail = \"richtf@usi.ch\",\nrole = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0002-0924-4613\"))", "Description": "Provides convenience functions to fetch standardized\nphylogenetic trees and per-tree provenance metadata from the\n'Phylo-Species Atlas'\n\ndirectly from R. The atlas is a curated collection of empirical\nspecies-level trees covering Bacteria, Archaea, and Eukaryota,\norganized into 62 partitions of life with tip labels normalized\nagainst a shared dictionary of standardized species\nidentifiers. Functions load any of the standardized trees with\nspecies labels resolved from the dictionary, list available\ntrees, and inspect per-tree provenance.", "License": "MIT + file LICENSE", "Encoding": "UTF-8", "URL": "https://github.com/franciscorichter/phylo-species-atlas,\nhttps://franciscorichter.github.io/phylo-species-atlas/", "BugReports": "https://github.com/franciscorichter/phylo-species-atlas/issues", "Config/testthat/edition": "3", "VignetteBuilder": "knitr", "RoxygenNote": "7.3.3", "Repository": "https://franciscorichter.r-universe.dev", "Date/Publication": "2026-05-31 14:45:55 UTC", "RemoteUrl": "https://github.com/franciscorichter/phylo-species-atlas", "RemoteRef": "HEAD", "RemoteSha": "66123e0019b27adf1d96a6190e21de3e5241314b", "RemoteSubdir": "phyloatlas", "NeedsCompilation": "no", "Packaged": { "Date": "2026-06-05 11:46:54 UTC", "User": "root" }, "Author": "Francisco Richter [aut, cre] (ORCID:\n)", "Maintainer": "Francisco Richter ", "MD5sum": "26bfcc84b470c29d70754dd9fe3da3d9", "_user": "franciscorichter", "_type": "src", "_file": "phyloatlas_0.1.0.tar.gz", "_fileid": "1bb35848cf9752905b158aee746264abc5a85ba498bcded8875979ec1931b7c2", "_filesize": 121426, "_sha256": "1bb35848cf9752905b158aee746264abc5a85ba498bcded8875979ec1931b7c2", "_created": "2026-06-05T11:46:54.000Z", "_published": "2026-06-05T11:49:35.721Z", "_distro": "noble", "_jobs": [ { "job": 79721030285, "time": 123, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7435787054" }, { "job": 79721030271, "time": 99, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7435780633" }, { "job": 79721030292, "time": 109, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7435782515" }, { "job": 79721030272, "time": 86, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7435776934" }, { "job": 79720666715, "time": 150, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7435751431" }, { "job": 79721030268, "time": 98, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7435780384" }, { "job": 79721030299, "time": 77, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7435774494" }, { "job": 79721030276, "time": 88, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7435777564" }, { "job": 79721030304, "time": 128, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7435788454" } ], "_buildurl": "https://github.com/r-universe/franciscorichter/actions/runs/27012901329", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/franciscorichter/phylo-species-atlas", "_commit": { "id": "66123e0019b27adf1d96a6190e21de3e5241314b", "author": "franciscorichter ", "committer": "franciscorichter ", "message": "phyloatlas: apply audit nice-to-have polish before CRAN submission\n\n- Network handling: new .try_url() helper in R/utils.R wraps all\n utils::read.csv()/ape::read.tree() calls with a 30s timeout and a\n graceful failure path (returns NULL + diagnostic message rather than\n throwing). list_trees() and atlas_info() now return NULL on network\n failure instead of propagating an error. CRAN policy: \"Packages which\n use Internet resources should fail gracefully if a resource is not\n available.\"\n- load_atlas_tree(): timeout enforced; error message classifies network\n failures vs. unknown-name failures.\n- Edge cases: .load_dictionary() warns on duplicate ids; list_trees()\n warns and returns an empty data frame if metadata.csv is empty.\n- DESCRIPTION: Description starts with \"Provides...\" per CRAN style.\n- Examples: simplified to use is.null() checks instead of try() (consistent\n with the new NULL-on-failure return contract).\n- Roxygen: @family atlas grouping on all four exported functions;\n atlas_clear_cache() now has a runnable @examples block (safe no-op).\n- @return docstrings made precise (column names, classes, NULL semantics).\n- Input validation: !is.na(name) added alongside nzchar checks.\n- .Rbuildignore: also exclude CRAN_AUDIT.md from the submission tarball.\n\nR CMD check --as-cran: 0 errors, 0 warnings, 2 expected first-submission\nNOTEs.\n", "time": 1780238755 }, "_maintainer": { "name": "Francisco Richter", "email": "richtf@usi.ch", "orcid": "0000-0002-0924-4613" }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.0", "role": "Depends" }, { "package": "ape", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" }, { "package": "withr", "role": "Suggests" } ], "_owner": "franciscorichter", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2026-15", "n": 5 }, { "week": "2026-19", "n": 1 }, { "week": "2026-20", "n": 36 }, { "week": "2026-21", "n": 49 }, { "week": "2026-22", "n": 6 } ], "_tags": [ { "name": "v1.0.0", "date": "2026-05-11" }, { "name": "v1.0.1", "date": "2026-05-11" }, { "name": "v1.0.2", "date": "2026-05-11" }, { "name": "v1.0.3", "date": "2026-05-12" }, { "name": "v1.0.4", "date": "2026-05-31" } ], "_stars": 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"atlas_info", "list_trees", "load_atlas_tree" ], "_help": [ { "page": "atlas_clear_cache", "title": "Clear the in-memory cache", "concept": [ "atlas" ], "topics": [ "atlas_clear_cache" ] }, { "page": "atlas_info", "title": "Get metadata for a single tree", "concept": [ "atlas" ], "topics": [ "atlas_info" ] }, { "page": "list_trees", "title": "List trees available in the Phylo-Species Atlas", "concept": [ "atlas" ], "topics": [ "list_trees" ] }, { "page": "load_atlas_tree", "title": "Load a tree from the Phylo-Species Atlas", "concept": [ "atlas" ], "topics": [ "load_atlas_tree" ] } ], "_readme": "https://github.com/franciscorichter/phylo-species-atlas/raw/HEAD/phyloatlas/README.md", "_rundeps": [ "ape", "digest", "lattice", "nlme", "Rcpp" ], "_vignettes": [ { "source": "phyloatlas.Rmd", "filename": "phyloatlas.html", "title": "Getting started with phyloatlas", "engine": "knitr::rmarkdown", "headings": [ "What this package does", "Loading a tree (offline demo)", "Loading a real atlas tree (requires network)", "Browsing available trees", "Pointing at a fork or local mirror", "Provenance and reproducibility", "Where to learn more" ], "created": "2026-05-31 14:33:55", "modified": "2026-05-31 14:33:55", "commits": 1 } ], "_score": 4.3979400086720375, "_indexed": true, "_nocasepkg": "phyloatlas", "_universes": [ "franciscorichter" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "0.1.0", "date": "2026-06-05T11:49:03.000Z", "distro": "noble", "commit": "66123e0019b27adf1d96a6190e21de3e5241314b", "fileid": "729b68980ea8f4a3f3dc8c99e34ba351323a6f404f21b2c3a57327eb3c563b64", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/franciscorichter/actions/runs/27012901329" }, { "r": "4.6.0", "os": "linux", "version": "0.1.0", "date": "2026-06-05T11:48:42.000Z", "distro": "noble", "commit": "66123e0019b27adf1d96a6190e21de3e5241314b", "fileid": "a80cb4c0c32c6bb487e40abe538fd8eb9d54f54015f66d49d7718d0ea81291e1", "status": "success", "check": 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