{ "_id": "6a1941b5acfb0bcc41dd7024", "Package": "AnVILPublish", "Title": "Publish Packages and Other Resources to AnVIL Workspaces", "Version": "1.22.0", "Authors@R": "c(\nperson(\n\"Marcel\", \"Ramos\", role = c(\"aut\", \"cre\"),\nemail = \"marcel.ramos@sph.cuny.edu\",\ncomment = c(ORCID = \"0000-0002-3242-0582\")\n),\nperson(\n\"Martin\", \"Morgan\", role = c(\"aut\"),\ncomment = c(ORCID = \"0000-0002-5874-8148\")\n),\nperson(\"Kayla\", \"Interdonato\", role = \"aut\"),\nperson(\n\"Vincent\", \"Carey\", role = \"ctb\",\ncomment = c(ORCID = \"0000-0003-4046-0063\")\n))", "Description": "Use this package to create or update AnVIL workspaces from\nresources such as R / Bioconductor packages. The metadata about\nthe package (e.g., select information from the package\nDESCRIPTION file and from vignette YAML headings) are used to\npopulate the 'DASHBOARD'. Vignettes are translated to python\nnotebooks ready for evaluation in AnVIL.", "License": "Artistic-2.0", "biocViews": "Infrastructure, Software", "Encoding": "UTF-8", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.3.3", "VignetteBuilder": "knitr", "Config/testthat/edition": "3", "Date": "2026-04-24", "Config/pak/sysreqs": "cmake make libicu-dev libsecret-1-dev libuv1-dev\nlibssl-dev libx11-dev zlib1g-dev", "Repository": "https://bioc-release.r-universe.dev", "Date/Publication": "2026-04-28 12:54:06 UTC", "RemoteUrl": "https://github.com/bioc/AnVILPublish", "RemoteRef": "RELEASE_3_23", "RemoteSha": "245d3082453fe05623b3fbbbba39de7667f8bb24", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-29 06:40:56 UTC", "User": "root" }, "Author": "Marcel Ramos [aut, cre] (ORCID:\n),\nMartin Morgan [aut] (ORCID: ),\nKayla Interdonato [aut],\nVincent Carey [ctb] (ORCID: )", "Maintainer": "Marcel Ramos ", "MD5sum": "fb237e9885d3cf82fca7dbdb11da0fba", "_user": "bioc-release", "_type": "src", "_file": "AnVILPublish_1.22.0.tar.gz", "_fileid": "be9adf8a3b74dbea1ab847bc79bc462cc64ec878518bb74490ee1fe92e1df834", "_filesize": 118593, "_sha256": "be9adf8a3b74dbea1ab847bc79bc462cc64ec878518bb74490ee1fe92e1df834", "_created": "2026-05-29T06:40:56.000Z", "_published": "2026-05-29T07:35:17.885Z", "_jobs": [ { "job": 78451240212, "time": 137, "config": "bioc-checks", "r": "4.6.0", "check": "ERROR", "artifact": "7284710819" }, { "job": 78451240220, "time": 199, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "7284725135" }, { "job": 78451240247, "time": 203, "config": "linux-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7284725999" }, { "job": 78451240201, "time": 100, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "7285508533" }, { "job": 78451240211, "time": 94, "config": "macos-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "7285508934" }, { "job": 78450831818, "time": 206, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7284678805" }, { "job": 78451240298, "time": 130, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7284708695" }, { "job": 78451240218, "time": 107, "config": "windows-devel", "r": "4.7.0", "check": "NOTE", "artifact": "7284703758" }, { "job": 78451240229, "time": 101, "config": "windows-oldrel", "r": "4.5.3", "check": "NOTE", "artifact": "7284702363" }, { "job": 78451240250, "time": 117, "config": "windows-release", "r": "4.6.0", "check": "NOTE", "artifact": "7284705976" } ], "_bioccheck": { "error": 3, "warning": 1, "note": 8 }, "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26622279013", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/AnVILPublish", "_commit": { "id": "245d3082453fe05623b3fbbbba39de7667f8bb24", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to even y prior to creation of RELEASE_3_23 branch\n", "time": 1777380846 }, "_maintainer": { "name": "Marcel Ramos", "email": "marcel.ramos@sph.cuny.edu", "login": "link-ny", "bluesky": "@mramos148.bsky.social", "linkedin": "in/mramos148", "orcid": "0000-0002-3242-0582", "twitter": "@M2RuseR", "description": "Sr. Data Scientist @ CUNY School of Public Health: Waldron Lab & Bioconductor Core Team Member / \nR 📦 dev ", "uuid": 4392950 }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "AnVIL", "role": "Imports" }, { "package": "AnVILGCP", "role": "Imports" }, { "package": "BiocBaseUtils", "role": "Imports" }, { "package": "BiocManager", "role": "Imports" }, { "package": "httr", "role": "Imports" }, { "package": "jsonlite", "role": "Imports" }, { "package": "rmarkdown", "role": "Imports" }, { "package": "yaml", "role": "Imports" }, { "package": "readr", "role": "Imports" }, { "package": "whisker", "role": "Imports" }, { "package": "tools", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "BiocStyle", "role": "Suggests" }, { "package": "GCPtools", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": false, "_usedby": 1, "_updates": [ { "week": "2025-33", "n": 2 }, { "week": "2025-44", "n": 2 }, { "week": "2026-12", "n": 3 }, { "week": "2026-17", "n": 4 }, { "week": "2026-18", "n": 1 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.23.0", "bioc": "3.24" }, { "branch": "release", "version": "1.22.0", "bioc": "3.23" } ], "_topics": [ "infrastructure", "software" ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 316, "source": "https://www.bioconductor.org/packages/stats/bioc/AnVILPublish" }, "_searchresults": 0, "_rbuild": "4.6.0", "_assets": [ "extra/AnVILPublish.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" ], "_realowner": "bioc", "_cranurl": false, "_exports": [ "add_access", "as_notebook", "as_workspace", "create_workspace" ], "_help": [ { "page": "add_access", "title": "Add Bioconductor_User group to workspace access", "topics": [ "add_access" ] }, { "page": "as_notebook", "title": "Render vignettes as .ipynb notebooks", "topics": [ "as_notebook" ] }, { "page": "as_workspace", "title": "Render R packages as AnVIL workspaces", "topics": [ "as_workspace" ] }, { "page": "AnVILPublish-utils", "title": "Create an AnVIL Workspace", "topics": [ "create_workspace" ] } ], "_readme": "https://github.com/bioc/AnVILPublish/raw/RELEASE_3_23/README.md", "_rundeps": [ "AnVIL", "AnVILBase", "AnVILGCP", "askpass", "base64enc", "BiocBaseUtils", "BiocManager", "bit", "bit64", "bslib", "cachem", "cli", "clipr", "commonmark", "cpp11", "crayon", "crosstalk", "curl", "digest", "dplyr", "DT", "evaluate", "fastmap", "filelock", "fontawesome", "formatR", "fs", "futile.logger", "futile.options", "GCPtools", "generics", "glue", "highr", "hms", "htmltools", "htmlwidgets", "httpuv", "httr", "httr2", "jquerylib", "jsonlite", "keyring", "knitr", "lambda.r", "later", "lazyeval", "lifecycle", "magrittr", "memoise", "mime", "miniUI", "openssl", "otel", "pillar", "pkgconfig", "prettyunits", "progress", "promises", "purrr", "R6", "rapiclient", "rappdirs", "Rcpp", "readr", "rlang", "rmarkdown", "sass", "shiny", "sourcetools", "stringi", "stringr", "sys", "tibble", "tidyr", "tidyselect", "tinytex", "tzdb", "utf8", "vctrs", "vroom", "whisker", "withr", "xfun", "xtable", "yaml" ], "_vignettes": [ { "source": "AnVILPublishIntro.Rmd", "filename": "AnVILPublishIntro.html", "title": "Publishing R / Bioconductor Packages To AnVIL Workspaces", "author": "Martin Morgan", "engine": "knitr::rmarkdown", "headings": [ "AnVILPublish", "Package installation", "Requirements", "Best practices", "The gcloud SDK", "Quarto software", "Creating or updating workspaces", "From package source", "From collections of Rmd files", "Updating notebooks or workspace permissions", "Updating workspace notebooks from vignettes", "Adding user access credentials to share the notebook", "Vignette and .Rmd best practices", "Orientation", "Additional notes on .Rmd conversion", "Session info" ], "created": "2020-08-17 21:58:19", "modified": "2025-08-12 19:26:04", "commits": 20 } ], "_score": 4.8750612633917, "_indexed": false, "_nocasepkg": "anvilpublish", "_universes": [ "bioc-release" ], "_indexurl": "https://bioc.r-universe.dev/AnVILPublish", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.22.0", "date": "2026-05-29T06:44:03.000Z", "distro": "noble", "commit": "245d3082453fe05623b3fbbbba39de7667f8bb24", "fileid": "9dc07f76550731c6ccf0c45f3e6702d5cfd0ade53412060abbad830758f79f53", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26622279013" }, { "r": "4.6.0", "os": "linux", "version": "1.22.0", "date": "2026-05-29T06:44:08.000Z", "distro": "noble", "commit": "245d3082453fe05623b3fbbbba39de7667f8bb24", "fileid": "5b0f5e000ffb6211710622c6cee59c3940381609e4ff2022be35e7b717d14a97", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26622279013" }, { "r": "4.5.3", "os": "mac", "version": "1.22.0", "date": "2026-05-29T07:34:40.000Z", "commit": "245d3082453fe05623b3fbbbba39de7667f8bb24", "fileid": "1dd642abe06a3d532d769962c2d477d48e28c324ece02c6b3f7f085bc4bd73a2", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26622279013" }, { "r": "4.6.0", "os": "mac", "version": "1.22.0", "date": "2026-05-29T07:34:39.000Z", "commit": "245d3082453fe05623b3fbbbba39de7667f8bb24", "fileid": "6ce760047e099f097a717e3b2dbb00cfa343f629eb869e86d75a048b76b61514", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26622279013" }, { "r": "4.6.0", "os": "wasm", "version": "1.22.0", "date": "2026-05-29T06:43:19.000Z", "commit": "245d3082453fe05623b3fbbbba39de7667f8bb24", "fileid": "c75d6220c323aaf3c7c8f2cbb01534415584fa97185951c654a9efa5a12fce72", "status": "success", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26622279013" }, { "r": "4.7.0", "os": "win", "version": "1.22.0", "date": "2026-05-29T06:42:26.000Z", "commit": "245d3082453fe05623b3fbbbba39de7667f8bb24", "fileid": "9cd3f1a069075f7d207b10a8e62360cc147a85f6ca272bbb493542152e42db1e", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26622279013" }, { "r": "4.5.3", "os": "win", "version": "1.22.0", "date": "2026-05-29T06:42:15.000Z", "commit": "245d3082453fe05623b3fbbbba39de7667f8bb24", "fileid": "6fa07b57dc342c556c915da8f619b3175cd4c3a08dd61d0a702e4de734a35c58", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26622279013" }, { "r": "4.6.0", "os": "win", "version": "1.22.0", "date": "2026-05-29T06:42:40.000Z", "commit": "245d3082453fe05623b3fbbbba39de7667f8bb24", "fileid": "d412833b731b0ade72d5b881274d695def803bd12909e8e2ddc9edf3f8271afe", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26622279013" } ] }