{ "_id": "6a3103b03efcd9bda435451d", "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": "https://bioc-release.r-universe.dev", "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": "2026-06-16 07:45:58 UTC", "User": "root" }, "Author": "Aaron Lun [aut, cre]", "Maintainer": "Aaron Lun ", "MD5sum": "23e39a2fd920cb18a962edb5073a2c99", "_user": "bioc-release", "_type": "src", "_file": "gypsum_1.8.0.tar.gz", "_fileid": "6f26bc7380eedad662fb479e038ab1c90361c6e059e731d0c6c2eef7c7dd17a4", "_filesize": 262138, "_sha256": "6f26bc7380eedad662fb479e038ab1c90361c6e059e731d0c6c2eef7c7dd17a4", "_created": "2026-06-16T07:45:58.000Z", "_published": "2026-06-16T08:05:04.209Z", "_jobs": [ { "job": 81606433461, "time": 147, "config": "bioc-checks", "r": "4.6.0", "check": "WARNING", "artifact": "7660467331" }, { "job": 81606433478, "time": 174, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "7660476981" }, { "job": 81606433462, "time": 159, "config": "linux-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7660471842" }, { "job": 81606433465, "time": 99, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "7660747567" }, { "job": 81606433456, "time": 112, "config": "macos-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "7660759416" }, { "job": 81605644041, "time": 279, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7660416028" }, { "job": 81606433500, "time": 110, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7660455102" }, { "job": 81606433483, "time": 93, "config": "windows-devel", "r": "4.7.0", "check": "NOTE", "artifact": "7660448954" }, { "job": 81606433480, "time": 98, "config": "windows-oldrel", "r": "4.5.3", "check": "NOTE", "artifact": "7660449384" }, { "job": 81606433487, "time": 113, "config": "windows-release", "r": "4.6.0", "check": "NOTE", "artifact": "7660455054" } ], "_bioccheck": { "error": 0, "warning": 2, "note": 8 }, "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27602179693", "_status": "success", "_host": "GitHub-Actions", "_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": "noble", "_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": 1, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 1 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.9.0", "bioc": "3.24" }, { "branch": "release", "version": "1.8.0", "bioc": "3.23" } ], "_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": 440, "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_devurl": "https://github.com/artifactdb/gypsum-r", "_searchresults": 20, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/gypsum.html", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "LICENSE", "manual.pdf" ], "_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": 4.778151250383644, "_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": "2026-06-16T07:50:20.000Z", "distro": "noble", "commit": "35d37418aedd2d391b46219b7ecf70881b45a81c", "fileid": "95c7d4c4c8752be7d407b802110c5255ada26cc47919e403c6c36815234d2a2a", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27602179693" }, { "r": "4.6.0", "os": "linux", "version": "1.8.0", "date": "2026-06-16T07:50:05.000Z", "distro": "noble", "commit": "35d37418aedd2d391b46219b7ecf70881b45a81c", "fileid": "222a7022e9c71042755779c89b0f0711de2ce57903ad660ab0dd3c9a02b37882", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27602179693" }, { "r": "4.5.3", "os": "mac", "version": "1.8.0", "date": "2026-06-16T08:03:42.000Z", "commit": "35d37418aedd2d391b46219b7ecf70881b45a81c", "fileid": "54de99b240753cce86231b5015dbb986cd78b0958b536bddf99b5285862f38cc", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27602179693" }, { "r": "4.6.0", "os": "mac", "version": "1.8.0", "date": "2026-06-16T08:04:14.000Z", "commit": "35d37418aedd2d391b46219b7ecf70881b45a81c", "fileid": "e6c05245195bc3e4c77d5f49c5b71f7f8ca530b3e796d5298a2e04e8450d06b4", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27602179693" }, { "r": "4.6.0", "os": "wasm", "version": "1.8.0", "date": "2026-06-16T07:49:47.000Z", "commit": "35d37418aedd2d391b46219b7ecf70881b45a81c", "fileid": "99c8820c4b28f0eb93cba5ab215f0fb5162f9e43080d26a7c18b1a60e08b4bb2", "status": "success", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27602179693" }, { "r": "4.7.0", "os": "win", "version": "1.8.0", "date": "2026-06-16T07:48:49.000Z", "commit": "35d37418aedd2d391b46219b7ecf70881b45a81c", "fileid": "24d95970c7e0cc301c38e2ee40110df1563f9f0df98f24d68eec388c8ccce60d", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27602179693" }, { "r": "4.5.3", "os": "win", "version": "1.8.0", "date": "2026-06-16T07:48:53.000Z", "commit": "35d37418aedd2d391b46219b7ecf70881b45a81c", "fileid": "2e5db067b2c102ec0ee40ccf0624c5b10ffd642070a53db3d9474b6bf689a31f", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27602179693" }, { "r": "4.6.0", "os": "win", "version": "1.8.0", "date": "2026-06-16T07:49:09.000Z", "commit": "35d37418aedd2d391b46219b7ecf70881b45a81c", "fileid": "5aa6a6f2ca82f9014686b323a5466a2a2f8f190c888b566d9b1aba816a83ea04", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27602179693" } ] }