{ "_id": "6acf324fd9de2f3f33fc8f88", "Package": "gypsum", "Version": "1.8.0", "Date": "2024-06-20", "Title": "Interface to the gypsum REST API", "Description": "Client for the gypsum REST API\n(https://gypsum.artifactdb.com), a cloud-based file store in\nthe ArtifactDB ecosystem. This package provides functions for\nuploads, downloads, and various adminstrative and management\ntasks. Check out the documentation at\nhttps://github.com/ArtifactDB/gypsum-worker for more details.", "Authors@R": "person(\"Aaron\", \"Lun\", role=c(\"aut\", \"cre\"), email=\"infinite.monkeys.with.keyboards@gmail.com\")", "License": "MIT + file LICENSE", "RoxygenNote": "7.3.1", "VignetteBuilder": "knitr", "URL": "https://github.com/ArtifactDB/gypsum-R", "BugReports": "https://github.com/ArtifactDB/gypsum-R/issues", "biocViews": "DataImport", "Config/pak/sysreqs": "libssl-dev", "Repository": "Bioconductor 3.23", "Date/Publication": "2026-04-28 13:02:20 UTC", "RemoteUrl": "https://github.com/bioc/gypsum", "RemoteRef": "RELEASE_3_23", "RemoteSha": "35d37418aedd2d391b46219b7ecf70881b45a81c", "NeedsCompilation": "no", "Packaged": { "Date": "2026-10-14 07:28:38 UTC", "User": "root" }, "Author": "Aaron Lun [aut, cre]", "Maintainer": "Aaron Lun ", "_user": "bioc-release", "_type": "src", "_file": "gypsum_1.8.0.tar.gz", "_fileid": "https://r2.ropensci.org/6ccd76518c1b61c5db9aee614a5117c3b579be16b285da19120bb31b9958d971", "_filesize": 262244, "_sha256": "6ccd76518c1b61c5db9aee614a5117c3b579be16b285da19120bb31b9958d971", "_expires": "2027-01-22T07:42:05.000Z", "_created": "2026-10-14T07:28:38.000Z", "_published": "2026-10-14T07:42:07.224Z", "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/38528167608", "_status": "success", "_host": "GitHub-Actions", "_bioccheck": { "error": 0, "warning": 2, "note": 8 }, "_upstream": "https://github.com/bioc/gypsum", "_commit": { "id": "35d37418aedd2d391b46219b7ecf70881b45a81c", "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": 1777381340 }, "_maintainer": { "name": "Aaron Lun", "email": "infinite.monkeys.with.keyboards@gmail.com", "login": "ltla", "twitter": "@realAaronLun", "description": "(ノಠ益ಠ)ノ彡┻━┻\n", "uuid": 8166669 }, "_distro": "resolute", "_jobs": [ { "job": 115734802387, "time": 134, "config": "bioc-checks", "r": "4.6.1", "check": "WARNING", "artifact": "11877296304" }, { "job": 115734802426, "time": 171, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "11876459125" }, { "job": 115734802320, "time": 183, "config": "linux-release-x86_64", "r": "4.6.1", "check": "NOTE", "artifact": "11877007251" }, { "job": 115734802296, "time": 121, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "11877945319" }, { "job": 115734802301, "time": 109, "config": "macos-release-arm64", "r": "4.6.1", "check": "NOTE", "artifact": "11877307742" }, { "job": 115733499951, "time": 222, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "11877001507" }, { "job": 115734802323, "time": 109, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "11876239162" }, { "job": 115734802346, "time": 94, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "11877076679" }, { "job": 115734802583, "time": 100, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "NOTE", "artifact": "11876374134" }, { "job": 115734802433, "time": 86, "config": "windows-release-x86_64", "r": "4.6.1", "check": "NOTE", "artifact": "11877151444" } ], "_registered": true, "_dependencies": [ { "package": "utils", "role": "Imports" }, { "package": "httr2", "role": "Imports" }, { "package": "jsonlite", "role": "Imports" }, { "package": "parallel", "role": "Imports" }, { "package": "filelock", "role": "Imports" }, { "package": "rappdirs", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "testthat", "role": "Suggests" }, { "package": "BiocStyle", "role": "Suggests" }, { "package": "digest", "role": "Suggests" }, { "package": "jsonvalidate", "role": "Suggests" }, { "package": "DBI", "role": "Suggests" }, { "package": "RSQLite", "role": "Suggests" }, { "package": "S4Vectors", "role": "Suggests" }, { "package": "methods", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": false, "_usedby": 10, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 1 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.9.0", "bioc": "3.24", "repository": "bioc" }, { "branch": "release", "version": "1.8.0", "bioc": "3.23", "repository": "bioc" } ], "_topics": [ "dataimport" ], "_stars": 1, "_contributors": [ { "user": "ltla", "count": 108, "uuid": 8166669 }, { "user": "jwokaty", "count": 2, "uuid": 1744257 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "followers": 477, "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 6417, "source": "https://www.bioconductor.org/packages/stats/bioc/gypsum" }, "_devurl": "https://github.com/artifactdb/gypsum-r", "_searchresults": 21, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/gypsum.html", "extra/manual.pdf", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "LICENSE" ], "_homeurl": "https://github.com/artifactdb/gypsum-r", "_realowner": "bioc", "_cranurl": false, "_exports": [ "abortUpload", "accessToken", "approveProbation", "cacheDirectory", "cloneVersion", "completeUpload", "createProject", "defineTextQuery", "fetchLatest", "fetchManifest", "fetchMetadataDatabase", "fetchMetadataSchema", "fetchPermissions", "fetchQuota", "fetchSummary", "fetchUsage", "formatObjectMetadata", "gsc", "listAssets", "listFiles", "listProjects", "listVersions", "prepareDirectoryUpload", "publicS3Config", "refreshLatest", "refreshUsage", "rejectProbation", "removeAsset", "removeProject", "removeVersion", "resolveLinks", "restUrl", "saveFile", "saveVersion", "searchMetadata", "searchMetadataFilter", "searchMetadataText", "searchMetadataTextFilter", "setAccessToken", "setPermissions", "setQuota", "startUpload", "translateTextQuery", "unlockProject", "uploadDirectory", "uploadFiles", "validateMetadata" ], "_help": [ { "page": "abortUpload", "title": "Abort an upload", "topics": [ "abortUpload" ] }, { "page": "accessToken", "title": "Get and set GitHub access tokens", "topics": [ "accessToken", "setAccessToken" ] }, { "page": "approveProbation", "title": "Approve a probational upload", "topics": [ "approveProbation" ] }, { "page": "cacheDirectory", "title": "Cache directory", "topics": [ "cacheDirectory" ] }, { "page": "cloneVersion", "title": "Clone a version's directory structure", "topics": [ "cloneVersion" ] }, { "page": "completeUpload", "title": "Complete an upload", "topics": [ "completeUpload" ] }, { "page": "createProject", "title": "Create a new project", "topics": [ "createProject" ] }, { "page": "fetchLatest", "title": "Fetch the latest version", "topics": [ "fetchLatest" ] }, { "page": "fetchManifest", "title": "Fetch version manifest", "topics": [ "fetchManifest" ] }, { "page": "fetchMetadataDatabase", "title": "Fetch a metadata database", "topics": [ "fetchMetadataDatabase" ] }, { "page": "fetchMetadataSchema", "title": "Fetch a metadata schema", "topics": [ "fetchMetadataSchema" ] }, { "page": "fetchPermissions", "title": "Fetch project permissions", "topics": [ "fetchPermissions" ] }, { "page": "fetchQuota", "title": "Fetch project quota details", "topics": [ "fetchQuota" ] }, { "page": "fetchSummary", "title": "Fetch version summary", "topics": [ "fetchSummary" ] }, { "page": "fetchUsage", "title": "Fetch project usage details", "topics": [ "fetchUsage" ] }, { "page": "formatObjectMetadata", "title": "Format object-related metadata", "topics": [ "formatObjectMetadata" ] }, { "page": "listAssets", "title": "List assets", "topics": [ "listAssets" ] }, { "page": "listFiles", "title": "List files for a version", "topics": [ "listFiles" ] }, { "page": "listProjects", "title": "List all projects", "topics": [ "listProjects" ] }, { "page": "listVersions", "title": "List asset versions", "topics": [ "listVersions" ] }, { "page": "prepareDirectoryUpload", "title": "Prepare to upload a directory", "topics": [ "prepareDirectoryUpload" ] }, { "page": "publicS3Config", "title": "Public S3 configuration", "topics": [ "publicS3Config" ] }, { "page": "refreshLatest", "title": "Refresh the latest version", "topics": [ "refreshLatest" ] }, { "page": "refreshUsage", "title": "Refresh the quota usage", "topics": [ "refreshUsage" ] }, { "page": "rejectProbation", "title": "Reject a probational upload", "topics": [ "rejectProbation" ] }, { "page": "removeAsset", "title": "Remove an asset", "topics": [ "removeAsset" ] }, { "page": "removeProject", "title": "Remove a project", "topics": [ "removeProject" ] }, { "page": "removeVersion", "title": "Remove a version of an asset", "topics": [ "removeVersion" ] }, { "page": "resolveLinks", "title": "Resolve links in the cache directory", "topics": [ "resolveLinks" ] }, { "page": "restUrl", "title": "URL for the REST API", "topics": [ "restUrl" ] }, { "page": "saveFile", "title": "Save a file from a version of a project asset", "topics": [ "saveFile" ] }, { "page": "saveVersion", "title": "Save all files for a version of a project asset", "topics": [ "saveVersion" ] }, { "page": "searchMetadata", "title": "Search the metadata database", "topics": [ "defineTextQuery", "gsc", "gypsum.search.clause", "Ops.gypsum.search.clause", "searchMetadata", "searchMetadataFilter", "searchMetadataText", "searchMetadataTextFilter" ] }, { "page": "setPermissions", "title": "Set project permissions", "topics": [ "setPermissions" ] }, { "page": "setQuota", "title": "Set project quota", "topics": [ "setQuota" ] }, { "page": "startUpload", "title": "Start an upload", "topics": [ "startUpload" ] }, { "page": "translateTextQuery", "title": "Translate a plain-text query to a gypsum.search.clause", "topics": [ "translateTextQuery" ] }, { "page": "unlockProject", "title": "Unlock a project", "topics": [ "unlockProject" ] }, { "page": "uploadDirectory", "title": "Upload a directory to the gypsum backend", "topics": [ "uploadDirectory" ] }, { "page": "uploadFiles", "title": "Upload files for a versioned asset", "topics": [ "uploadFiles" ] }, { "page": "validateMetadata", "title": "Validate metadata against a JSON schema", "topics": [ "validateMetadata" ] } ], "_readme": "https://github.com/bioc/gypsum/raw/RELEASE_3_23/README.md", "_rundeps": [ "askpass", "cli", "curl", "filelock", "glue", "httr2", "jsonlite", "lifecycle", "magrittr", "openssl", "R6", "rappdirs", "rlang", "sys", "vctrs", "withr" ], "_vignettes": [ { "source": "userguide.Rmd", "filename": "userguide.html", "title": "Interacting with the gypsum REST API", "author": "Aaron Lun", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Reading files", "Uploading files", "Basic usage", "Link generation", "Changing permissions", "Probational uploads", "Inspecting the quota", "Validating metadata", "Administration", "Session information" ], "created": "2023-12-06 00:24:43", "modified": "2024-04-03 00:05:55", "commits": 8 } ], "_score": 6.606672588744773, "_indexed": false, "_nocasepkg": "gypsum", "_universes": [ "bioc-release" ], "_indexurl": "https://bioc.r-universe.dev/gypsum", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.8.0", "date": "2026-10-14T07:31:18.000Z", "distro": "resolute", "commit": "35d37418aedd2d391b46219b7ecf70881b45a81c", "fileid": "https://r2.ropensci.org/97743157f105ebb19e8c843549b6de827b72f8532b9b4bf6b0b10aad13d2ea6e", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/38528167608" }, { "r": "4.6.1", "os": "linux", "version": "1.8.0", "date": "2026-10-14T07:31:30.000Z", "distro": "resolute", "commit": "35d37418aedd2d391b46219b7ecf70881b45a81c", "fileid": "https://r2.ropensci.org/b391fb3958b5b3cd2e317556cc54c58ff64e82998a8ce64f89d39cbc64f032f4", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/38528167608" }, { "r": "4.5.3", "os": "mac", "version": "1.8.0", "date": "2026-10-14T07:41:13.000Z", "commit": "35d37418aedd2d391b46219b7ecf70881b45a81c", "fileid": "https://r2.ropensci.org/e144b53e99e01ffaa01b5ac05060b054055cf9e7568d170979a7c4b76dc91a45", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/38528167608" }, { "r": "4.6.1", "os": "mac", "version": "1.8.0", "date": "2026-10-14T07:37:35.000Z", "commit": "35d37418aedd2d391b46219b7ecf70881b45a81c", "fileid": "https://r2.ropensci.org/9a8373aae1aefcdf9b4f7d40a84e47ef907e69fdde47ef81edecd931c0d11bcb", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/38528167608" }, { "r": "4.6.0", "os": "wasm", "version": "1.8.0", "date": "2026-10-14T07:30:49.000Z", "commit": "35d37418aedd2d391b46219b7ecf70881b45a81c", "fileid": "https://r2.ropensci.org/e66e2ec15a03f7e8edd8de8a91e1faac5ef4d15c9de098d8a7ffff9a11cb14bf", "status": "success", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/38528167608" }, { "r": "4.7.0", "os": "win", "version": "1.8.0", "date": "2026-10-14T07:30:00.000Z", "commit": "35d37418aedd2d391b46219b7ecf70881b45a81c", "fileid": "https://r2.ropensci.org/4e1cac6f4aede67f3222512c11ae443b074d5c4b474faffdfba8c1659d2abe3b", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/38528167608" }, { "r": "4.5.3", "os": "win", "version": "1.8.0", "date": "2026-10-14T07:30:01.000Z", "commit": "35d37418aedd2d391b46219b7ecf70881b45a81c", "fileid": "https://r2.ropensci.org/a2e0395ccb35a34d98c8802f1e7997c4b638d7eb7e06d11ede6702691bf47bd9", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/38528167608" }, { "r": "4.6.1", "os": "win", "version": "1.8.0", "date": "2026-10-14T07:29:49.000Z", "commit": "35d37418aedd2d391b46219b7ecf70881b45a81c", "fileid": "https://r2.ropensci.org/65c57bb4676b3cfcacfa4af062bc0adafce02c6d78a5257fa201ecea539fd7de", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/38528167608" } ] }