{ "_id": "6ac855b0de46216d5edd4575", "Package": "OmicsMLRepoR", "Type": "Package", "Title": "Search harmonized metadata created under the OmicsMLRepo project", "Version": "1.6.1", "Date": "2026-10-08", "Authors@R": "c(person(given = \"Sehyun\",\nfamily = \"Oh\",\nrole = c(\"aut\", \"cre\"),\nemail = \"shbrief@gmail.com\",\ncomment = c(ORCID = \"0000-0002-9490-3061\")),\nperson(given = \"Kaelyn\",\nfamily = \"Long\",\nemail = \"krlong586@gmail.com\",\nrole = \"aut\"))", "Description": "This package provides functions to browse the harmonized\nmetadata for large omics databases. This package also supports\ndata navigation if the metadata incorporates ontology.", "License": "Artistic-2.0", "biocViews": "Software, Infrastructure, DataRepresentation", "Encoding": "UTF-8", "RoxygenNote": "7.3.3", "VignetteBuilder": "knitr", "URL": "https://github.com/shbrief/OmicsMLRepoR", "BugReports": "https://github.com/shbrief/OmicsMLRepoR/issues", "Config/pak/sysreqs": "cmake libglpk-dev make libicu-dev libuv1-dev\nlibxml2-dev libssl-dev libx11-dev", "Repository": "Bioconductor 3.23", "Date/Publication": "2026-10-08 21:06:12 UTC", "RemoteUrl": "https://github.com/bioc/OmicsMLRepoR", "RemoteRef": "RELEASE_3_23", "RemoteSha": "361dd537395bfcc2ec5f71609e67cbc1d5ddbbcb", "NeedsCompilation": "no", "Packaged": { "Date": "2026-10-09 02:30:20 UTC", "User": "root" }, "Author": "Sehyun Oh [aut, cre] (ORCID: ),\nKaelyn Long [aut]", "Maintainer": "Sehyun Oh ", "_user": "bioc-release", "_type": "src", "_file": "OmicsMLRepoR_1.6.1.tar.gz", "_fileid": "https://r2.ropensci.org/fbcfb1ea6aac6dcd00f83643be2ac26410a428b81cebde2a85ce6e9586472d1d", "_filesize": 363567, "_sha256": "fbcfb1ea6aac6dcd00f83643be2ac26410a428b81cebde2a85ce6e9586472d1d", "_expires": "2027-01-17T02:47:10.000Z", "_created": "2026-10-09T02:30:20.000Z", "_published": "2026-10-09T02:47:12.072Z", "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/37874459829", "_status": "success", "_host": "GitHub-Actions", "_bioccheck": { "error": 0, "warning": 1, "note": 6 }, "_upstream": "https://github.com/bioc/OmicsMLRepoR", "_commit": { "id": "361dd537395bfcc2ec5f71609e67cbc1d5ddbbcb", "author": "Sehyun Oh ", "committer": "Sehyun Oh ", "message": "retry transient OLS failures to stabilize the vignette build\n\nThe build failed with \"HTTP 500 Internal Server Error\" while knitting\nQuickstart.Rmd. tree_filter() issues one live OLS query per search term\n(~14 across the vignette), so a single transient 5xx from the service\nfails the whole build.\n\n o getOntoInfo() retries requests that fail for a transient reason -\n HTTP 5xx, dropped connections, timeouts - with an exponential\n backoff (new `retries` argument). Client errors still fail fast.\n o Quickstart.Rmd probes OLS once and skips the OLS-dependent chunks\n when the service is unreachable, so an outage no longer fails the\n build. The remaining chunks still render.\n o test-tree_filter.R skips, rather than fails, the OLS-dependent\n tests when the service is unavailable.\n o version bump\n\nCo-Authored-By: Claude Opus 5 (1M context) \n", "time": 1791493572 }, "_maintainer": { "name": "Sehyun Oh", "email": "shbrief@gmail.com", "login": "shbrief", "linkedin": "in/sehyunoh", "twitter": "@drsehyun", "description": "Molecular Biologist & Bioinformatician", "uuid": 15724490, "orcid": "0000-0002-9490-3061" }, "_distro": "resolute", "_jobs": [ { "job": 113641184336, "time": 205, "config": "bioc-checks", "r": "4.6.1", "check": "WARNING", "artifact": "11592091803" }, { "job": 113641184403, "time": 334, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "11591873983" }, { "job": 113641184327, "time": 319, "config": "linux-release-x86_64", "r": "4.6.1", "check": "NOTE", "artifact": "11592330561" }, { "job": 113641184441, "time": 158, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", 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"2026-05", "n": 1 }, { "week": "2026-06", "n": 1 }, { "week": "2026-07", "n": 2 }, { "week": "2026-11", "n": 4 }, { "week": "2026-12", "n": 3 }, { "week": "2026-18", "n": 1 }, { "week": "2026-41", "n": 1 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.7.0", "bioc": "3.24", "repository": "bioc" }, { "branch": "release", "version": "1.6.0", "bioc": "3.23", "repository": "bioc" } ], "_topics": [ "software", "infrastructure", "datarepresentation", "u24ca289073" ], "_stars": 2, "_contributors": [ { "user": "shbrief", "count": 212, "uuid": 15724490 }, { "user": "krlong68", "count": 48, "uuid": 95976790 }, { "user": "jwokaty", "count": 8, "uuid": 1744257 }, { "user": "copilot", "count": 2, "uuid": 198982749 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "followers": 474, "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 209, "source": "https://www.bioconductor.org/packages/stats/bioc/OmicsMLRepoR" }, "_devurl": "https://github.com/shbrief/omicsmlrepor", "_searchresults": 20, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/manual.pdf", "extra/NEWS.html", "extra/NEWS.txt", "extra/OmicsMLRepoR.html", "extra/readme.html", "extra/readme.md" ], "_homeurl": "https://github.com/shbrief/omicsmlrepor", "_realowner": "bioc", "_cranurl": false, "_exports": [ "availableTerms", "get_ontologies", "getLongMetaTb", "getMetadata", "getNarrowMetaTb", "getOntoInfo", "getShortMetaTb", "getWideMetaTb", "merge_vectors", "ontoSummarize", "ontoTreePlot", "spreadMeta", "tree_filter" ], "_datasets": [ { "name": "mini_cbio", "title": "A subset of cBioPortalData metadata", "object": "mini_cbio", "file": "mini_cbio.RData", "class": [ "data.frame" ], "fields": [ "curation_id", "acronym", "acronym_ontology_term_id", "sex", "package", "treatment_name", "treatment_name_ontology_term_id", "treatment_type", "treatment_type_ontology_term_id" ], "rows": 10, "table": true, "tojson": true }, { "name": "mini_cmd", "title": "A subset of cMD metadata", "object": "mini_cmd", "file": "mini_cmd.RData", "class": [ "spec_tbl_df", "tbl_df", "tbl", "data.frame" ], "fields": [ "curation_id", "hla", "package" ], "rows": 200, "table": true, "tojson": true }, { "name": "mini_cmd2", "title": "A subset of cMD metadata", "object": "mini_cmd2", "file": "mini_cmd2.RData", "class": [ "data.frame" ], "fields": [ "curation_id", "target_condition", "target_condition_ontology_term_id", "pmid", "disease", "disease_ontology_term_id", "package" ], "rows": 200, "table": true, "tojson": true }, { "name": "mini_cmd3", "title": "A subset of cMD metadata", "object": "mini_cmd3", "file": "mini_cmd3.RData", "class": [ "data.frame" ], "fields": [ "curation_id", "pmid", "package", "target_condition", "feces_phenotype", "probing_pocket_depth", "target_condition_ontology_term_id", "feces_phenotype_ontology_term_id", "probing_pocket_depth_ontology_term_id" ], "rows": 10, "table": true, "tojson": true }, { "name": "sample_metadata", "title": "sample_metadata", "object": "sample_metadata", "file": "sample_metadata.RData", "class": [ "spec_tbl_df", "tbl_df", "tbl", "data.frame" ], "fields": [ "curation_id", "curated_sex", "curated_sex_ontology_term_id", "curated_disease", "curated_disease_ontology_term_id", "package", "last_updated" ], "rows": 4, "table": true, "tojson": true } ], "_help": [ { "page": "availableTerms", "title": "Extract all the terms used in a quired attribute/column", "topics": [ "availableTerms" ] }, { "page": "get_ontologies", "title": "Extract ontology from the ontology term ids", "topics": [ "get_ontologies" ] }, { "page": "getLongMetaTb", "title": "Expands metadata with multiple values belong to a same attribute", "topics": [ "getLongMetaTb" ] }, { "page": "getMetadata", "title": "Download a harmonized metadata table", "topics": [ "getMetadata" ] }, { "page": "getNarrowMetaTb", "title": "Collapse values from multiple columns into one", "topics": [ "getNarrowMetaTb" ] }, { "page": "getOntoInfo", "title": "Query Ontology Lookup Service (OLS)", "topics": [ "getOntoInfo" ] }, { "page": "getShortMetaTb", "title": "Compresses expanded metadata columns to one row per sample", "topics": [ "getShortMetaTb" ] }, { "page": "getWideMetaTb", "title": "Create individual columns for different attributes stored in one column", "topics": [ "getWideMetaTb" ] }, { "page": "merge_vectors", "title": "Custom function to merge vectors", "topics": [ "merge_vectors" ] }, { "page": "mini_cbio", "title": "A subset of cBioPortalData metadata", "topics": [ "mini_cbio" ] }, { "page": "mini_cmd", "title": "A subset of cMD metadata", "topics": [ "mini_cmd" ] }, { "page": "mini_cmd2", "title": "A subset of cMD metadata", "topics": [ "mini_cmd2" ] }, { "page": "mini_cmd3", "title": "A subset of cMD metadata", 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