{ "_id": "6abebf5c99f7aa8c6aa5773b", "Package": "Rclade", "Title": "Automated Deep-Time Phylogenetic Tree Collapsing and\nVisualization", "Version": "1.1.5", "Authors@R": "person(\"Zeng\", \"Zichao\", email = \"zengzichao@sjtu.edu.cn\",\nrole = c(\"aut\", \"cre\"))", "Author": "Zeng Zichao [aut, cre]", "Maintainer": "Zeng Zichao ", "Description": "Provides a single-function pipeline for automated\ncollapsing and visualization of large phylogenetic trees with\ngeological timescales. Automatically parses taxonomic labels\nfrom multiple formats (GTDB, Silva, NCBI, embedded, custom),\nidentifies Most Recent Common Ancestors (MRCAs), assigns\ncolor-blind-safe palettes, executes batch collapsing with\nautomatic nesting-aware ordering, integrates 'deeptime'\ngeologic time scales with adaptive time breaks and unit\nswitching, and manages smart legend layout. Supports special\nancestral node identifiers (LUCA, LACA, LBCA) for highlighting\nkey nodes in the tree of life. Provides external taxonomy file\nsupport for trees with incomplete or missing taxonomic labels.\nFeatures real-time logging with timestamps, step tracking, and\nmultiple log levels. Includes comprehensive input validation\nfor tree and sequence file formats. Reduces a 60-line manual\nworkflow to a single function call while preserving full\ncompatibility with the 'ggtree'/'deeptime' ecosystem. The\nvisualization pipeline builds on 'ggtree' Yu et al. (2017)\n, 'deeptime' Gearty (2025)\n, and 'ape' Paradis and\nSchliep (2019) .", "License": "MIT + file LICENSE", "Encoding": "UTF-8", "Roxygen": "list(markdown = TRUE)", "VignetteBuilder": "knitr", "Config/roxygen2/version": "8.0.0", "Config/testthat/edition": "3", "URL": "https://github.com/zengzichao/Rclade,\nhttps://zengzichao.github.io/Rclade/", "BugReports": "https://github.com/zengzichao/Rclade/issues", "Config/pak/sysreqs": "libcairo2-dev cmake libfontconfig1-dev\nlibfreetype6-dev make libicu-dev libjpeg-dev libpng-dev\nlibuv1-dev libxml2-dev libssl-dev", "Repository": "https://zengzichao.r-universe.dev", "Date/Publication": "2026-10-01 13:38:30 UTC", "RemoteUrl": "https://github.com/zengzichao/rclade", "RemoteRef": "HEAD", "RemoteSha": "9a1a6288be471bd6abfea3e9ad9a3774030985bc", "NeedsCompilation": "no", "Packaged": { "Date": "2026-10-01 19:54:00 UTC", "User": "root" }, "_user": "zengzichao", "_type": "src", "_file": "Rclade_1.1.5.tar.gz", "_fileid": "https://r2.ropensci.org/5acbb1520f785fc5d2431165605a792e0700643c88cbb79cd02879d8cdc44d13", "_filesize": 1063026, "_sha256": "5acbb1520f785fc5d2431165605a792e0700643c88cbb79cd02879d8cdc44d13", "_expires": "2027-01-09T20:15:21.000Z", "_created": "2026-10-01T19:54:00.000Z", "_published": "2026-10-01T20:15:24.174Z", "_jobs": [ { "job": 110555698071, "time": 217, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "11191350569" }, { "job": 110555698292, "time": 217, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "11190606471" }, { "job": 110555698105, "time": 130, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "11190923871" }, { "job": 110555698022, "time": 133, "config": "macos-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "11191028292" }, { "job": 110552934376, "time": 406, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "11190227137" }, { "job": 110555698025, "time": 150, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "11190247531" }, { "job": 110555698056, "time": 136, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "11191135751" }, { "job": 110555698172, "time": 145, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "11191095849" }, { "job": 110555698156, "time": 142, "config": "windows-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "11190392553" } ], "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/zengzichao/actions/runs/36916848654", "_status": "success", "_upstream": "https://github.com/zengzichao/rclade", "_commit": { "id": "9a1a6288be471bd6abfea3e9ad9a3774030985bc", "author": "Zichao Zeng ", "committer": "GitHub ", "message": "fix(ci): macOS 矩阵回退 macos-15 并补齐日常维护配置 (#7)\n\n* fix(ci): macOS 矩阵回退 macos-15 并补齐日常维护配置\n\n- R-CMD-check: macos-latest 固定为 macos-15。9 月下旬 macos-26-arm64\n 新镜像上 install_local 秒级失败，且 quiet=TRUE 吞掉了错误细节；\n 新增非阻塞 macos-26-compat 探针 job，以 verbose 输出持续跟踪根因\n- 所有 install_local 去 quiet，失败时可从 CI 日志定位真实错误\n- actions/checkout v4→v5（原生 Node 24，消除 Node 20 弃用警告，本 PR 验证）、\n codecov-action v4→v7、JamesIves/github-pages-deploy-action 4.5.0→4.9.0\n- 触发分支移除不存在的 master；R-CMD-check 增加 workflow_dispatch\n- dependabot 新增 docker 生态跟踪 Dockerfile 基础镜像\n- 新增 SECURITY.md、CODEOWNERS、Issue 模板、PR 模板\n\n* fix(ci): 移除冗余的 any::svglite，根治 macOS job 崩溃\n\n根因（2026-10-01 verbose 日志取证）：\n- install_local 在 'byte-compile and prepare package for lazy loading'\n 阶段崩溃：gdtools 0.5.1（RSPM macOS binary，9 月下旬新构建）的\n gdtools.so 硬链接 /opt/X11/lib/libXrender.1.dylib（XQuartz），\n 新 runner 镜像不再提供该路径，dlopen 失败\n- gdtools 唯一引入路径是 workflow extra-packages 的 any::svglite，\n 而 R/、tests/、scripts/、NAMESPACE 均不使用 svglite（冗余依赖）\n- 对照证据：不含 svglite 的 deps-smoke / coverage 全平台绿，\n 含 svglite 的 macos-15 与 macos-26 job 同样失败（1m42s / 2m2s）\n\n修复：R-CMD-check（matrix 与 macos-26-compat 探针）、functional-tests\n移除 any::svglite，保留注释说明根因，防止回归。\n\n* fix(ci): macOS job 显式安装 XQuartz，修复 gdtools dlopen 失败\n\n进一步取证（移除 any::svglite 后 macOS 仍失败，且 gdtools 0.5.1 仍被新装）：\n- 真实依赖链是硬依赖：Rclade -> ggtree -> ggiraph -> gdtools\n （依赖解析日志中 ggiraph 的 dependencies 列表含 gdtools）\n- gdtools 的 RSPM macOS binary (0.5.1, 9 月下旬构建) 硬链接\n /opt/X11/lib/libXrender.1.dylib，新版 runner 镜像不再自带 XQuartz\n- 因此任何 library(Rclade) 路径在 macOS 上都会 dlopen 失败；\n 移除 svglite 只能去掉冗余，无法切断 ggtree 的硬依赖链\n- ubuntu 一直绿：Linux binary 链接系统库，无此问题\n\n修复：macOS job 在 setup-r 前用 brew 安装 xquartz 提供 /opt/X11。\n（svglite 移除保留：它仍是仓库未使用的冗余依赖）\n\n* fix(ci): 恢复 any::svglite——SVG 输出测试（O-003）确实需要它\n\n第三轮验证结论：XQuartz 修复后 macos-26 探针全过，macos-15 推进到\nself-test 阶段，57/58 通过，唯一失败 O-003: SVG output——\nsave_timetree() 走 ggsave(device = 'svg')，而 ggplot2 的 svg 设备\n硬性要求 svglite 包。前一轮把它当冗余移除是误判（静态 grep 看不到\n经 ggplot2 的间接依赖）；ubuntu 之所以仍绿是旧库缓存里残留了 svglite。\n\n终态方案：svglite 显", "time": 1790861910 }, "_maintainer": { "name": "Zeng Zichao", "email": "zengzichao@sjtu.edu.cn", "login": "zengzichao", "description": "", "uuid": 301673815 }, "_distro": "resolute", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.1.0", "role": "Depends" }, { "package": "ape", "version": ">= 5.0", "role": "Imports" }, { "package": "ggtree", "version": ">= 4.0.0", "role": "Imports" }, { "package": "deeptime", "version": ">= 1.0", "role": "Imports" }, { "package": "ggplot2", "version": ">= 3.5.0", "role": "Imports" }, { "package": "rlang", "role": "Imports" }, { "package": "stringr", "version": ">= 1.5", "role": "Imports" }, { "package": "tidytree", "version": ">= 0.4", "role": "Imports" }, { "package": "viridisLite", "role": "Imports" }, { "package": "treeio", "version": ">= 1.0", "role": "Suggests" }, { "package": "phangorn", "version": ">= 2.0", "role": "Suggests" }, { "package": "RColorBrewer", "role": "Suggests" }, { "package": "cowplot", "version": ">= 1.1", "role": "Suggests" }, { "package": "patchwork", "version": ">= 1.1", "role": "Suggests" }, { "package": "shiny", "version": ">= 1.7", "role": "Suggests" }, { "package": 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"Example phylogenetic tree with polytomies", "object": "polytomy_tree", "file": "polytomy_tree.rda", "class": [ "phylo" ], "fields": [], "table": false, "tojson": false } ], "_help": [ { "page": "batch_plot", "title": "Batch plot timetrees from a directory of tree files", "topics": [ "batch_plot" ] }, { "page": "check_monophyly", "title": "Check if a taxonomic group is monophyletic", "topics": [ "check_monophyly" ] }, { "page": "check_special_monophyly", "title": "Check if a special identifier corresponds to a monophyletic group", "topics": [ "check_special_monophyly" ] }, { "page": "detect_taxonomy_format", "title": "Detect taxonomy format from tip labels", "topics": [ "detect_taxonomy_format" ] }, { "page": "example_tree", "title": "Example phylogenetic tree with GTDB-style labels", "topics": [ "example_tree" ] }, { "page": "get_supported_extensions", "title": "Get supported file extensions", "topics": [ "get_supported_extensions" ] }, { "page": "parse_taxonomy", "title": "Unified taxonomy parsing entry point", "topics": [ "parse_taxonomy" ] }, { "page": "plot_timetree", "title": "Plot a phylogenetic tree with geological timescale and taxonomic collapsing", "topics": [ "plot_timetree" ] }, { "page": "polytomy_tree", "title": "Example phylogenetic tree with polytomies", "topics": [ "polytomy_tree" ] }, { "page": "rclade_logo", "title": "Display Rclade ASCII art logo", "topics": [ "rclade_logo" ] }, { "page": "rclade_options", "title": "Construct a validated options list for 'plot_timetree()'", "topics": [ "rclade_options" ] }, { "page": "read_taxonomy_file", "title": "Read taxonomy information from a table file", "topics": [ "read_taxonomy_file" ] }, { "page": "read_tree_auto", "title": "Read tree from file with automatic format detection", "topics": [ "read_tree_auto" ] }, { "page": "run_rclade_cli", "title": "Run Rclade from the command line", "topics": [ "run_rclade_cli" ] }, { "page": "run_rclade_selftest", "title": "Run Rclade self-test", "topics": [ "run_rclade_selftest" ] }, { "page": "run_rclade_shiny", "title": "Launch Rclade Shiny app", "topics": [ "run_rclade_shiny" ] }, { "page": "save_session_info", "title": "Save sessionInfo() for reproducibility", "topics": [ "save_session_info" ] }, { "page": "save_timetree", "title": "Save a timetree plot to file", "topics": [ "save_timetree" ] }, { "page": "set_log_enabled", "title": "Enable or disable logging", "topics": [ "set_log_enabled" ] }, { "page": "set_log_file", "title": "Set log file for dual output", "topics": [ "set_log_file" ] }, { "page": "set_log_level", "title": "Set log level", "topics": [ "set_log_level" ] }, { "page": "summarize_taxonomy_quality", "title": "Report taxonomy label parsing quality", "topics": [ "summarize_taxonomy_quality" ] }, { "page": "summarize_taxonomy_quality_with_file", "title": "Summarize taxonomy quality with external file support", "topics": [ "summarize_taxonomy_quality_with_file" ] }, { "page": "summarize_timetree", "title": "Print a 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