{ "_id": "6a1ae5301d7bb097a09efdd6", "Package": "metabolomicsWorkbenchR", "Type": "Package", "Title": "Metabolomics Workbench in R", "Version": "1.23.0", "Authors@R": "c(\nperson(\nc(\"Gavin\",\"Rhys\"),\n\"Lloyd\",\nrole=c(\"aut\",\"cre\"),\nemail=\"g.r.lloyd@bham.ac.uk\"),\nperson(\nc(\"Ralf\",\"Johannes\", \"Maria\"),\n\"Weber\",\nrole=c(\"aut\"),\nemail=\"r.j.weber@bham.ac.uk\")\n)", "Description": "This package provides functions for interfacing with the\nMetabolomics Workbench RESTful API. Study, compound, protein\nand gene information can be searched for using the API. Methods\nto obtain study data in common Bioconductor formats such as\nSummarizedExperiment and MultiAssayExperiment are also\nincluded.", "License": "GPL-3", "Encoding": "UTF-8", "RoxygenNote": "7.3.1", "Collate": "'parse_fcns.R' 'generics.R' 'class_def.R' 'constants.R'\n'helper_fcns.R' 'metabolomicsWorkbenchR.R'", "VignetteBuilder": "knitr", "biocViews": "Software, Metabolomics", "Config/pak/sysreqs": "libicu-dev libssl-dev zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:53:30 UTC", "RemoteUrl": "https://github.com/bioc/metabolomicsWorkbenchR", "RemoteRef": "HEAD", "RemoteSha": "5bac27b0d1e26c2e01f62117ba093c9b5a5160fc", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-30 09:35:16 UTC", "User": "root" }, "Author": "Gavin Rhys Lloyd [aut, cre],\nRalf Johannes Maria Weber [aut]", "Maintainer": "Gavin Rhys Lloyd ", "MD5sum": "87e175e42f85dfdec646994e134cfade", "_user": "bioc", "_type": "src", "_file": "metabolomicsWorkbenchR_1.23.0.tar.gz", "_fileid": "13fbfc4a52525c4f07eb639119446f7267f7e777a80eb2b725aee07d0cd8235b", "_filesize": 2053501, "_sha256": "13fbfc4a52525c4f07eb639119446f7267f7e777a80eb2b725aee07d0cd8235b", "_created": "2026-05-30T09:35:16.000Z", "_published": "2026-05-30T13:25:03.996Z", "_jobs": [ { "job": 78640029867, "time": 214, "config": "bioc-checks", "r": "4.6.0", "check": "NOTE", "artifact": "7307326042" }, { "job": 78640029865, "time": 407, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "7307344083" }, { "job": 78640029859, "time": 374, "config": "linux-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7307341173" }, { "job": 78640029861, "time": 197, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "7308494357" }, { "job": 78640029864, "time": 196, "config": "macos-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "7308494192" }, { "job": 78639401896, "time": 258, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7307220642" }, { "job": 78640029892, "time": 143, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7307319257" }, { "job": 78640029885, "time": 228, "config": "windows-devel", "r": "4.7.0", "check": "NOTE", "artifact": "7307321518" }, { "job": 78640029881, "time": 204, "config": "windows-oldrel", "r": "4.5.3", "check": "NOTE", "artifact": "7307319095" }, { "job": 78640029886, "time": 264, "config": "windows-release", "r": "4.6.0", "check": "NOTE", "artifact": "7307325051" } ], "_bioccheck": { "error": 0, "warning": 0, "note": 11 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26675820903", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/metabolomicsWorkbenchR", "_commit": { "id": "5bac27b0d1e26c2e01f62117ba093c9b5a5160fc", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777380810 }, "_maintainer": { "name": "Gavin Rhys Lloyd", "email": "g.r.lloyd@bham.ac.uk", "login": "grlloyd", "description": "Experimental Officer in Biostatistics, Phenome Centre Birmingham", "uuid": 12222440 }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.0", "role": "Depends" }, { "package": "data.table", "role": "Imports" }, { "package": "httr", "role": "Imports" }, { "package": "jsonlite", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "MultiAssayExperiment", "role": "Imports" }, { "package": "struct", "role": "Imports" }, { "package": "SummarizedExperiment", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "BiocStyle", "role": "Suggests" }, { "package": "covr", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "HDF5Array", "role": "Suggests" }, { "package": "httptest", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "structToolbox", "role": "Suggests" }, { "package": "testthat", "role": "Suggests" }, { "package": "pmp", "role": "Suggests" }, { "package": "grid", "role": "Suggests" }, { "package": "png", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.23.0", "bioc": "3.24" }, { "branch": "release", "version": "1.22.0", "bioc": "3.23" } ], "_topics": [ "software", "metabolomics" ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 392, "source": "https://www.bioconductor.org/packages/stats/bioc/metabolomicsWorkbenchR" }, "_searchresults": 13, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/metabolomicsWorkbenchR.html", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_realowner": "bioc", "_cranurl": false, "_exports": [ "check_pattern", "check_puts", "context", "context_inputs", "context_outputs", "do_query", "input_example", "input_item", "is_valid", "output_item" ], "_help": [ { "page": "mw_base", "title": "Get slot value from mw_base objects", "topics": [ "$,mw_base-method" ] }, { "page": "check_pattern", "title": "Check input against acceptable input pattern", "topics": [ "check_pattern", "check_pattern,mw_input_item-method" ] }, { "page": "check_puts", "title": "Check inputs/outputs match", "topics": [ "check_puts", "check_puts,mw_input_item-method" ] }, { "page": "context", "title": "Contexts", "topics": [ "context" ] }, { "page": "context_inputs", "title": "Valid inputs", "topics": [ "context_inputs" ] }, { "page": "context_outputs", "title": "Valid outputs", "topics": [ "context_outputs" ] }, { "page": "do_query", "title": "Query the Metabolomics Workbench database", "topics": [ "do_query", "do_query,character,character,character,character-method", "do_query,character,character,character,missing-method", "do_query,mw_context,mw_input_item,character,mw_DE_item-method", "do_query,mw_context,mw_input_item,character,mw_MAE_item-method", "do_query,mw_context,mw_input_item,character,mw_output_item-method", "do_query,mw_context,mw_input_item,character,mw_SE_item-method", "do_query,mw_context,mw_input_item,character,mw_untarg_DE_item-method", "do_query,mw_context,mw_input_item,character,mw_untarg_SE_item-method", "do_query,mw_exactmass_context,character,character,missing-method", "do_query,mw_exactmass_context,list,character,character-method", "do_query,mw_exactmass_context,list,character,missing-method", "do_query,mw_exactmass_context,list,character,mw_output_item-method", "do_query,mw_moverz_context,character,character,missing-method", "do_query,mw_moverz_context,list,character,character-method", "do_query,mw_moverz_context,list,character,missing-method", "do_query,mw_moverz_context,list,character,mw_output_item-method" ] }, { "page": "input_example", "title": "Valid input_value for input_item", "topics": [ "input_example" ] }, { "page": "input_item", "title": "Input items", "topics": [ "input_item" ] }, { "page": "is_valid", "title": "Check validity of context and inputs/outputs", "topics": [ "is_valid", "is_valid,mw_context,character,character,character-method", "is_valid,mw_exactmass_context,character,character,missing-method", "is_valid,mw_moverz_context,character,character,missing-method" ] }, { "page": "output_item", "title": "Output items", "topics": [ "output_item" ] } ], "_readme": "https://github.com/bioc/metabolomicsWorkbenchR/raw/HEAD/README.md", "_rundeps": [ "abind", "askpass", "Biobase", "BiocBaseUtils", "BiocGenerics", "cli", "cpp11", "curl", "data.table", "DelayedArray", "dplyr", "evaluate", "generics", "GenomicRanges", "glue", "highr", "httr", "httr2", "IRanges", "jsonlite", "knitr", "lattice", "lifecycle", "magrittr", "Matrix", "MatrixGenerics", "matrixStats", "mime", "MultiAssayExperiment", "openssl", "pillar", "pkgconfig", "purrr", "R6", "rappdirs", "rlang", "S4Arrays", "S4Vectors", "Seqinfo", "SparseArray", "stringi", "stringr", "struct", "SummarizedExperiment", "sys", "tibble", "tidyr", "tidyselect", "utf8", "vctrs", "withr", "xfun", "XVector", "yaml" ], "_vignettes": [ { "source": "example_using_structToolbox.Rmd", "filename": "example_using_structToolbox.html", "title": "Example using structToolbox", "author": "Gavin R Lloyd, Ralf J Weber", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Installation", "Querying the database", "Choosing a study", "Workflow", "Session Info" ], "created": "2021-02-23 10:55:17", "modified": "2023-09-25 14:38:32", "commits": 4 }, { "source": "Introduction_to_metabolomicsWorkbenchR.Rmd", "filename": "Introduction_to_metabolomicsWorkbenchR.html", "title": "Introduction to metabolomicsWorkbenchR", "author": "Gavin R Lloyd, Ralf J Weber", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Installation", "Running a query", "Special cases", "input_item \"ignored\"", "output_item \"compound_exact\", \"protein_exact\" and \"gene_exact\"", "output_item \"protein_partial\" and \"gene_partial\"", "output_item \"SummarizedExperiment\" and \"DatasetExperiment\"", "output_item \"MultiAssayExperiment\"", "output_item \"untarg_SummarizedExperiment\" and \"untarg_DatasetExperiment\"", "S4 classes", "Contexts", "Input / Output Items", "Session Info" ], "created": "2020-06-19 13:48:13", "modified": "2023-09-25 14:38:32", "commits": 6 } ], "_score": 4.414973347970818, "_indexed": true, "_nocasepkg": "metabolomicsworkbenchr", "_universes": [ "bioc", "grlloyd" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.23.0", "date": "2026-05-30T09:53:57.000Z", "distro": "noble", "commit": "5bac27b0d1e26c2e01f62117ba093c9b5a5160fc", "fileid": "4a6f65479e7b93af585e5fecf532c3534d02fab11ad3d211de393e513b02d130", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26675820903" }, { "r": "4.6.0", "os": "linux", "version": "1.23.0", "date": "2026-05-30T09:53:27.000Z", "distro": "noble", "commit": "5bac27b0d1e26c2e01f62117ba093c9b5a5160fc", "fileid": "dee456f8997f0a66bf18c453715caa2498f0d32aaabd0cdfe926210ed1775ff3", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26675820903" }, { "r": "4.5.3", "os": "mac", "version": "1.23.0", "date": "2026-05-30T13:23:07.000Z", "commit": "5bac27b0d1e26c2e01f62117ba093c9b5a5160fc", "fileid": "e7af9e5731531439056c9463db8652953a1ac562c59ba48a470cd656de7f6a1a", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26675820903" }, { "r": "4.6.0", "os": "mac", "version": "1.23.0", "date": "2026-05-30T13:22:47.000Z", "commit": "5bac27b0d1e26c2e01f62117ba093c9b5a5160fc", "fileid": "d354f4ce20b2cdebe7a710bcb9cf576ea3ff0a5c8b7932a86080fb363e789d54", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26675820903" }, { "r": "4.6.0", "os": "wasm", "version": "1.23.0", "date": "2026-05-30T09:52:12.000Z", "commit": "5bac27b0d1e26c2e01f62117ba093c9b5a5160fc", "fileid": "998580102c1dd2bd6bde086e13ab830209bb497c88be277baa016571640bc474", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26675820903" }, { "r": "4.7.0", "os": "win", "version": "1.23.0", "date": "2026-05-30T09:50:16.000Z", "commit": "5bac27b0d1e26c2e01f62117ba093c9b5a5160fc", "fileid": "06850722658186a547885287978d466f3bd258efff685194ac913f81a830515c", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26675820903" }, { "r": "4.5.3", "os": "win", "version": "1.23.0", "date": "2026-05-30T09:50:14.000Z", "commit": "5bac27b0d1e26c2e01f62117ba093c9b5a5160fc", "fileid": "502bd88e2911ea1154663db14cc2db154bc76d5769226a6e77b4c40ef3527196", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26675820903" }, { "r": "4.6.0", "os": "win", "version": "1.23.0", "date": "2026-05-30T09:50:33.000Z", "commit": "5bac27b0d1e26c2e01f62117ba093c9b5a5160fc", "fileid": "6a7a3d2eef2487cd9584142a5b5b333a671f7d59c92a7a7b4faf58c75c8313e3", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26675820903" } ] }