{ "_id": "6a1f355cb401979e73428662", "Package": "augere.core", "Version": "0.99.3", "Date": "2026-04-11", "Title": "Core Utilities for Automatically Generated Reports", "Description": "Provides utility functions for automatic generation of\nreports in the augere framework. This mostly involves parsing\nand dynamically editing Rmarkdown files, controlling inputs\ninto the augere pipelines. Each pipeline generates and executes\na self-contained Rmarkdown file for a common bioinformatics\nanalysis; see downstream packages like augere.de and\naugere.screen for examples of some analysis pipelines.", "Authors@R": "person(\"Aaron\", \"Lun\", role=c(\"cre\", \"aut\"), email=\"infinite.monkeys.with.keyboards@gmail.com\", comment=c(ORCID=\"0000-0002-3564-4813\"))", "License": "MIT + file LICENSE", "VignetteBuilder": "knitr", "RoxygenNote": "7.3.3", "Encoding": "UTF-8", "biocViews": "WorkflowManagement, ReportWriting", "URL": "https://github.com/augere-bioinfo/augere.core", "BugReports": "https://github.com/augere-bioinfo/augere.core/issues", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-05-14 22:17:52 UTC", "RemoteUrl": "https://github.com/bioc/augere.core", "RemoteRef": "HEAD", "RemoteSha": "892e35cd9e777f8a1b3a59daef63b6c227b906b4", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-15 06:34:20 UTC", "User": "root" }, "Author": "Aaron Lun [cre, aut] (ORCID: )", "Maintainer": "Aaron Lun ", "MD5sum": "fbb1eb6682a45c81a1becf27a68dbc78", "_user": "bioc", "_type": "src", "_file": "augere.core_0.99.3.tar.gz", "_fileid": "76eddde5a0a2c5fb1acc07816f95ae5e6e985361b6baaaf92bb590ced569f202", "_filesize": 146835, "_sha256": "76eddde5a0a2c5fb1acc07816f95ae5e6e985361b6baaaf92bb590ced569f202", "_created": "2026-05-15T06:34:20.000Z", "_published": "2026-06-02T19:56:12.247Z", "_jobs": [ { "job": 79159637336, "time": 161, "config": "bioc-checks", "r": "4.6.0", "check": "WARNING", "artifact": "7011519711" }, { "job": 79159637786, "time": 162, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7011518763" }, { "job": 79159637740, "time": 166, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7011519482" }, { "job": 79159637597, "time": 94, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7011516433" }, { "job": 79159637366, "time": 91, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7011512782" }, { "job": 79159636677, "time": 237, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7011483618" }, { "job": 79159636703, "time": 112, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7368340280" }, { "job": 79159637430, "time": 149, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7011515837" }, { "job": 79159637814, "time": 112, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7011508031" }, { "job": 79159637890, "time": 87, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7011502844" } ], "_bioccheck": { "error": 0, "warning": 1, "note": 5 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/25903982515", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/augere.core", "_commit": { "id": "892e35cd9e777f8a1b3a59daef63b6c227b906b4", "author": "LTLA ", "committer": "LTLA ", "message": "Added links to the BioC build reports.\n", "time": 1778797072 }, "_maintainer": { "name": "Aaron Lun", "email": "infinite.monkeys.with.keyboards@gmail.com", "login": "ltla", "orcid": "0000-0002-3564-4813", "twitter": "@realAaronLun", "uuid": 8166669 }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "utils", "role": "Imports" }, { "package": "grDevices", "role": "Imports" }, { "package": "testthat", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "BiocStyle", "role": "Suggests" }, { "package": "limma", "role": "Suggests" }, { "package": "edgeR", "role": "Suggests" }, { "package": "airway", "role": "Suggests" }, { "package": "S4Vectors", "role": "Suggests" }, { "package": "SummarizedExperiment", "role": "Suggests" }, { "package": "jsonlite", "role": "Suggests" }, { "package": "alabaster.base", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 4, "_updates": [ { "week": "2025-42", "n": 4 }, { "week": "2025-43", "n": 2 }, { "week": "2025-44", "n": 2 }, { "week": "2025-45", "n": 2 }, { "week": "2025-46", "n": 5 }, { "week": "2025-49", "n": 1 }, { "week": "2026-02", "n": 1 }, { "week": "2026-06", "n": 1 }, { "week": "2026-15", "n": 2 }, { "week": "2026-20", "n": 1 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "0.99.3", "bioc": "3.24" } ], "_topics": [ "workflowmanagement", "reportwriting" ], "_stars": 0, "_contributors": [ { "user": "ltla", "count": 21, "uuid": 8166669 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 32, "source": "https://www.bioconductor.org/packages/stats/bioc/augere.core" }, "_devurl": "https://github.com/augere-bioinfo/augere.core", "_searchresults": 0, "_rbuild": "4.6.0", "_assets": [ "extra/augere.core.html", "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/augere-bioinfo/augere.core", "_realowner": "bioc", "_cranurl": false, "_exports": [ "compileReport", "deparseToString", "evaluateChunks", "extractChunks", "parseRmdTemplate", "processInputCommands", "readResult", "replacePlaceholders", "resetInputCache", "saveResult", "wrapInput", "writeRmd" ], "_help": [ { "page": "augere.core-package", "title": "augere.core: Core Utilities for Automatically Generated Reports", "topics": [ "augere.core-package", "augere.core" ] }, { "page": "compileReport", "title": "Compile an Rmarkdown report", "topics": [ "compileReport" ] }, { "page": "deparseToString", "title": "Deparse object to a string", "topics": [ "deparseToString" ] }, { "page": "evaluateChunks", "title": "Evaluate R chunks", "topics": [ "evaluateChunks" ] }, { "page": "extractChunks", "title": "Extract R chunks", "topics": [ "extractChunks" ] }, { "page": "parseRmdTemplate", "title": "Parse Rmarkdown template", "topics": [ "parseRmdTemplate" ] }, { "page": "processInputCommands", "title": "Process commands for a pipeline input", "topics": [ "augere.input", "processInputCommands", "resetInputCache", "wrapInput" ] }, { "page": "replacePlaceholders", "title": "Substitute placeholders", "topics": [ "replacePlaceholders" ] }, { "page": "saveResult", "title": "Save a DE result", "topics": [ "readResult", "saveResult" ] }, { "page": "writeRmd", "title": "Write Rmarkdown file", "topics": [ "writeRmd" ] } ], "_readme": "https://github.com/bioc/augere.core/raw/HEAD/README.md", "_rundeps": [], "_vignettes": [ { "source": "userguide.Rmd", "filename": "userguide.html", "title": "Automatic generation of analysis reports", "author": "Aaron Lun", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Quick start", "Writing the template", "Representing data inputs", "Computing results", "Session information" ], "created": "2025-11-09 00:06:55", "modified": "2026-01-08 07:24:43", "commits": 3 } ], "_score": 5.778151250383644, "_indexed": true, "_nocasepkg": "augere.core", "_universes": [ "bioc", "ltla", "augere-bioinfo" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "0.99.3", "date": "2026-05-15T06:37:06.000Z", "distro": "noble", "commit": "892e35cd9e777f8a1b3a59daef63b6c227b906b4", "fileid": "345e9e4e95230973800d79b75c81f25e72ebdf1cb6a5ddcf443a39b1ce7d1f32", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/25903982515" }, { "r": "4.6.0", "os": "linux", "version": "0.99.3", "date": "2026-05-15T06:37:11.000Z", "distro": "noble", "commit": "892e35cd9e777f8a1b3a59daef63b6c227b906b4", "fileid": "e8b54c8aeb617dc59171a42f8d0fd849758ba58e281a9c52f6971fa4e8b33169", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/25903982515" }, { "r": "4.5.3", "os": "mac", "version": "0.99.3", "date": "2026-05-15T06:36:58.000Z", "commit": "892e35cd9e777f8a1b3a59daef63b6c227b906b4", "fileid": "cc673fff3a0f2f2b51759767b4b3f27d4c761ae7cb194d0d1dbfd13a8c050239", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/25903982515" }, { "r": "4.6.0", "os": "mac", "version": "0.99.3", "date": "2026-05-15T06:36:43.000Z", "commit": "892e35cd9e777f8a1b3a59daef63b6c227b906b4", "fileid": "f6f1d612f6bc32c5a6cb5bd992d9d713c0bc7d45eebbabcbf4abe9c5efcaa027", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/25903982515" }, { "r": "4.7.0", "os": "win", "version": "0.99.3", "date": "2026-05-15T06:36:25.000Z", "commit": "892e35cd9e777f8a1b3a59daef63b6c227b906b4", "fileid": "b8cf95547646d08d604b03f19b0a9c13fbc2ca4c6d1aa797b64f1413e1d3da4e", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/25903982515" }, { "r": "4.5.3", "os": "win", "version": "0.99.3", "date": "2026-05-15T06:36:09.000Z", "commit": "892e35cd9e777f8a1b3a59daef63b6c227b906b4", "fileid": "5d186d497dddfb24570454fc958d3e428d4dbbd5e487d28c9a0bb49c62b1701b", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/25903982515" }, { "r": "4.6.0", "os": "win", "version": "0.99.3", "date": "2026-05-15T06:35:44.000Z", "commit": "892e35cd9e777f8a1b3a59daef63b6c227b906b4", "fileid": "95d811f0772c47551fe9b42428325b73a22452bd1746ec9d922cb1dff8b9d049", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/25903982515" }, { "r": "4.6.0", "os": "wasm", "version": "0.99.3", "date": "2026-06-02T19:55:52.000Z", "commit": "892e35cd9e777f8a1b3a59daef63b6c227b906b4", "fileid": "fdf6887017e0e25f48c0a57cc6f20ee85e03db62ad7956da98bde5a7f04fa38b", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/25903982515" } ] }