{ "_id": "6a1051beacfb0bcc41ca152c", "Package": "ume", "Title": "Ultrahigh-Resolution Mass Spectrometry Data Evaluation for\nComplex Organic Matter", "Version": "1.6.1", "Authors@R": "c(\nperson(\"Boris\", \"Koch\",\nemail = \"boris.koch@awi.de\",\nrole = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0002-8453-731X\")),\nperson(\"Stephan\", \"Frickenhaus\",\nrole = \"ctb\",\ncomment = c(ORCID = \"0000-0002-0356-9791\")),\nperson(\"Oliver\", \"Lechtenfeld\",\nrole = \"ctb\",\ncomment = c(ORCID = \"0000-0001-5313-6014\")),\nperson(\"Tim\", \"Leefmann\",\nrole = \"ctb\",\ncomment = c(ORCID = \"0000-0002-5784-8657\")),\nperson(\"Fabian\", \"Moye\",\nrole = \"ctb\",\ncomment = c(ORCID = \"0000-0002-4632-5033\"))\n)", "Description": "Provides tools for assigning molecular formulas from exact\nmasses obtained by ultrahigh-resolution mass spectrometry. The\nmethodology follows the workflow described in Leefmann et al.\n(2019) . The package supports the\ninspection, filtering and visualization of molecular formula\ndata and includes utilities for calculating common molecular\nparameters (e.g., double bond equivalents, DBE). A graphical\nuser interface is available via the 'shiny'-based 'ume'\napplication.", "URL": "https://gitlab.awi.de/bkoch/ume, https://ume.awi.de/,\nhttps://www.awi.de/en/ume", "License": "MIT + file LICENSE", "Encoding": "UTF-8", "LazyData": "true", "LazyDataCompression": "xz", "RoxygenNote": "7.3.3", "VignetteBuilder": "knitr", "Config/testthat/edition": "3", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-09 17:52:37 UTC", "User": "root" }, "Author": "Boris Koch [aut, cre] (ORCID:\n), Stephan Frickenhaus\n[ctb] (ORCID: ), Oliver\nLechtenfeld [ctb] (ORCID:\n), Tim Leefmann [ctb]\n(ORCID: ), Fabian Moye\n[ctb] (ORCID: )", "Maintainer": "Boris Koch ", "Repository": "https://cran.r-universe.dev", "Date/Publication": "2026-05-09 17:16:31 UTC", "RemoteUrl": "https://github.com/cran/ume", "RemoteRef": "HEAD", "RemoteSha": "4adb3eb2ffe34311080c4e9312245a04e9c3e405", "MD5sum": "c33348c176fbd060bcdb35a861e8433c", "_user": "cran", "_type": "src", "_file": "ume_1.6.1.tar.gz", "_fileid": 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"author": "Boris Koch ", "committer": "cran-robot ", "message": "version 1.6.1\n", "time": 1778346991 }, "_maintainer": { "name": "Boris Koch", "email": "boris.koch@awi.de", "orcid": "0000-0002-8453-731X" }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.2.0", "role": "Depends" }, { "package": "data.table", "role": "Imports" }, { "package": "ggplot2", "role": "Imports" }, { "package": "plotly", "role": "Imports" }, { "package": "vegan", "role": "Imports" }, { "package": "viridis", "role": "Imports" }, { "package": "jsonlite", "role": "Imports" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "pander", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" }, { "package": "xml2", "role": "Suggests" }, { "package": "pdftools", "role": "Suggests" } ], "_owner": "cran", "_selfowned": false, "_usedby": 0, "_updates": [ { "week": "2025-50", "n": 1 }, { "week": "2026-19", "n": 1 } ], "_tags": [ { "name": "1.5.2", "date": "2025-12-12" }, { "name": "1.6.1", "date": "2026-05-09" } ], "_stars": 0, "_userbio": { "uuid": 6899542, "type": "organization", "name": "cran", "description": "Unofficial read-only mirror of all CRAN R packages" }, "_downloads": { "count": 147, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/ume" }, "_searchresults": 0, "_rbuild": "4.6.0", "_assets": [ "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", "extra/ume.html", "manual.pdf" ], "_realowner": "cran", "_cranurl": false, "_releases": [ { "version": "1.5.2", "date": "2025-12-12" }, { "version": "1.6.1", "date": "2026-05-09" } ], "_exports": [ "add_known_mf", "add_missing_element_columns", "as_peaklist", "assign_formulas", "calc_data_summary", "calc_dbe", "calc_eval_params", "calc_exact_mass", "calc_ideg", "calc_isotope_pattern", "calc_iterr", "calc_ma", "calc_ma_abs", "calc_neutral_mass", "calc_nm", "calc_norm_int", "calc_number_assignment", "calc_pielou_evenness", "calc_recalibrate_ms", "calc_shannon_index", "calc_simpson_index", "check_neutral_mf", "classify_files", "color.palette", "convert_data_table_to_molecular_formulas", "convert_molecular_formula_to_data_table", "create_custom_formula_library", "create_isotope_expanded_table", "create_ume_formula_library", "download_library", "eval_isotopes", "filter_int", "filter_mass_accuracy", "filter_mf_data", "get_isotope_info", "inchi_to_mf", "is_ume_peaklist", "order_columns", "remove_blanks", "remove_empty_columns", "subset_known_mf", "theme_uplots", "ume_assign_formulas", "ume_filter_formulas", "uplot_cluster", "uplot_cvm", "uplot_dbe_minus_o_freq", "uplot_dbe_vs_c", "uplot_dbe_vs_ma", "uplot_freq", "uplot_freq_ma", "uplot_freq_vs_ppm", "uplot_hc_vs_m", "uplot_heteroatoms", "uplot_isotope_precision", "uplot_kmd", "uplot_lcms", "uplot_ma_vs_mz", "uplot_ms", "uplot_n_mf_per_sample", "uplot_pca", "uplot_ratios", "uplot_reproducibility", "uplot_ri_vs_sample", "uplot_vk", "ustats_outlier" ], "_datasets": [ { "name": "known_mf", "title": "Collection of known formulas, for which additional information is available.", "object": "known_mf", "class": [ "data.table", "data.frame" ], "fields": [ "mf_kf_id", "mf", "category", "info1", "info2", "info3", "info4", "reference", "cas", "mw", "mass", "created_at", "last_update", "category_id" ], "rows": 302476, "table": true, "tojson": true }, { "name": "lib_demo", "title": "Demo formula library (200 - 300 Da, neutral mass)", "object": "lib_demo", "class": [ "data.table", "data.frame" ], "fields": [ "vkey", "mf", "mass", "12C", "13C", "1H", "14N", "15N", "16O", "31P", "32S", "34S" ], "rows": 115111, "table": true, "tojson": true }, { "name": "masses", "title": "Masses: Elements and isotopes", "object": "masses", "class": [ "data.table", "data.frame" ], "fields": [ "label", "symbol", "nm", "exact_mass", "mole_fraction", "relative_abundance", "valence", "valence2", "hill_order" ], "rows": 288, "table": true, "tojson": true }, { "name": "mf_data_demo", "title": "mf_data_demo", "object": "mf_data_demo", "class": [ "data.table", "data.frame" ], "fields": [ "file_id", "file", "peak_id", "mz", "i_magnitude", "norm_int", "m", "m_cal", "ppm", "nm", "mf", "dbe", "12C", "1H", "14N", "16O", "31P", "32S", "hc", "oc", "nc", "sc", "ai", "z", "kmd", "ppm_filt", "mf_id", "int15n", "int34s", "int13c", "s_n", "res", "del", "dev_n_c", "dbe_o", "nosc", "delg0_cox", "relint13c_calc", "int13c_calc", "relint34s_calc", "int34s_calc", "snp_check", "nsp_type", "co_tot", "nsp_tot", "n_occurrence_orig", "n_assignments_orig", "int_bp", "n_assignments", "int_ref" ], "rows": 9245, "table": true, "tojson": true }, { "name": "nice_labels_dt", "title": "nice_labels_dt", "object": "nice_labels_dt", "class": [ "data.table", "data.frame" ], "fields": [ "name_pattern", "name_substitute" ], "rows": 56, "table": true, "tojson": true }, { "name": "peaklist_demo", "title": "Demo peak list", "object": "peaklist_demo", "class": [ "data.table", "data.frame" ], "fields": [ "file_id", "file", "peak_id", "mz", "i_magnitude", "s_n", "res" ], "rows": 31091, "table": true, "tojson": true }, { "name": "tab_ume_labels", "title": "Labels of UME columns.", "object": "tab_ume_labels", "class": [ "data.table", "data.frame" ], "fields": [ "label_id", "label", "nice_label", "use_in_ume" ], "rows": 22, "table": true, "tojson": true }, { "name": "ume_logo_raster", "title": "Internal raster of the UME logo", "object": "ume_logo_raster", "class": [ "array" ], "fields": [], "table": false, "tojson": true } ], "_help": [ { "page": "add_known_mf", "title": "Add metainformation derived from ume::known_mf", "concept": [ "Formula assignment" ], "topics": [ "add_known_mf" ] }, { "page": "add_missing_element_columns", "title": "Add Missing Isotope Columns to mfd", "concept": [ "tools" ], "topics": [ "add_missing_element_columns" ] }, { "page": "as_peaklist", "title": "Check format of peaklist", "concept": [ "check ume objects" ], "topics": [ "as_peaklist" ] }, { "page": "assign_formulas", "title": "Molecular Formula Assignment", "topics": [ "assign_formulas" ] }, { "page": "calc_data_summary", "title": "Create a Data Summary Table for Element Ratios and Parameters", "concept": [ "calculations" ], "topics": [ "calc_data_summary" ] }, { "page": "calc_dbe", "title": "Calculate Double Bond Equivalent (DBE)", "concept": [ "calculations" ], "topics": [ "calc_dbe" ] }, { "page": "calc_eval_params", "title": "Calculate UME Evaluation Parameters", "concept": [ "Formula assignment", "calculations" ], "topics": [ "calc_eval_params" ] }, { "page": "calc_exact_mass", "title": "Calculate Exact Monoisotopic Mass of a Molecule", "concept": [ "calculations" ], "topics": [ "calc_exact_mass" ] }, { "page": "calc_ideg", "title": "Calculate Degradation Index (Ideg)", "concept": [ "calculations" ], "topics": [ "calc_ideg" ] }, { "page": "calc_isotope_pattern", "title": "Calculate Isotope Pattern", "concept": [ "isotopes" ], "topics": [ "calc_isotope_pattern" ] }, { "page": "calc_iterr", "title": "Calculate terrestrial indeces Iterr and Iterr2 (after Medeiros et al. 2016)", "concept": [ "index calculations" ], "topics": [ "calc_iterr" ] }, { "page": "calc_ma", "title": "Calculate mass accuracy", "concept": [ "calculations" ], "topics": [ "calc_ma" ] }, { "page": "calc_ma_abs", "title": "Calculate absolute mass accuracy range (ma)", "topics": [ "calc_ma_abs" ] }, { "page": "calc_neutral_mass", "title": "Calculate neutral molecular mass", "concept": [ "calculations" ], "topics": [ "calc_neutral_mass" ] }, { "page": "calc_nm", "title": "Calculate Nominal Mass of a Molecule", "concept": [ "calculations" ], "topics": [ "calc_nm" ] }, { "page": "calc_norm_int", "title": "Calculate Normalized Peak Intensities", "concept": [ "calculations" ], "topics": [ "calc_norm_int" ] }, { "page": "calc_number_assignment", "title": "Calculate Number of Molecular Formula Assignments per Peak", "concept": [ "calculations" ], "topics": [ "calc_number_assignment" ] }, { "page": "calc_pielou_evenness", "title": "Calculate Pielou's Evenness", "topics": [ "calc_pielou_evenness" ] }, { "page": "calc_shannon_index", "title": "Calculate the Shannon Diversity Index", "topics": [ "calc_shannon_index" ] }, { "page": "calc_simpson_index", "title": "Calculate the Simpson Diversity Index", "topics": [ "calc_simpson_index" ] }, { "page": "check_neutral_mf", "title": "Check neutral molecular formulas", "concept": [ "molecular formula functions" ], "topics": [ "check_neutral_mf" ] }, { "page": "classify_files", "title": "Classify FTMS files into categories based on filename patterns", "concept": [ "helper" ], "topics": [ "classify_files" ] }, { "page": "color.palette", "title": "Create a Custom Interpolated Color Palette", "topics": [ "color.palette" ] }, { "page": "convert_data_table_to_molecular_formulas", "title": "Convert Data Table with Element Counts to Molecular Formulas", "concept": [ "molecular formula functions" ], "topics": [ "convert_data_table_to_molecular_formulas" ] }, { "page": "convert_molecular_formula_to_data_table", "title": "Convert Molecular Formulas to a Data Table of Element Counts", "concept": [ "molecular formula functions" ], "topics": [ "convert_molecular_formula_to_data_table" ] }, { "page": "create_isotope_expanded_table", "title": "Create an Expanded Table of Parent and Isotope Daughter Formulas", "concept": [ "isotopes" ], "topics": [ "create_isotope_expanded_table" ] }, { "page": "create_ume_formula_library", "title": "Create a molecular formula library for UME", "topics": [ "create_ume_formula_library" ] }, { "page": "download_library", "title": "Download and Load a UME Formula Library from Zenodo", "topics": [ "download_library" ] }, { "page": "eval_isotopes", "title": "Evaluate isotope information", "concept": [ "Formula assignment", "isotopes" ], "topics": [ "eval_isotopes" ] }, { "page": "filter_int", "title": "Filter by (relative) peak magnitude", "concept": [ "Formula subsetting" ], "topics": [ "filter_int" ] }, { "page": "filter_mass_accuracy", "title": "Automated filter for mass accuracy", "concept": [ "Formula subsetting" ], "topics": [ "filter_mass_accuracy" ] }, { "page": "filter_mf_data", "title": "Filter molecular formula data by mass spectrometric metadata", "concept": [ "Formula subsetting" ], "topics": [ "filter_mf_data" ] }, { "page": "get_isotope_info", "title": "Retrieve NIST element and isotope data", "topics": [ "get_isotope_info" ] }, { "page": "inchi_to_mf", "title": "Extract molecular formula from InChI string", "topics": [ "inchi_to_mf" ] }, { "page": "is_ume_peaklist", "title": "Check whether an object is a UME peaklist", "topics": [ "is_ume_peaklist" ] }, { "page": "known_mf", "title": "Collection of known formulas, for which additional information is available.", "concept": [ "ume data" ], "topics": [ "known_mf" ] }, { "page": "lib_demo", "title": "Demo formula library (200 - 300 Da, neutral mass)", "concept": [ "ume data" ], "topics": [ "lib_demo" ] }, { "page": "masses", "title": "Masses: Elements and isotopes", "concept": [ "ume data" ], "topics": [ "masses" ] }, { "page": "mf_data_demo", "title": "mf_data_demo", "concept": [ "ume data" ], "topics": [ "mf_data_demo" ] }, { "page": "nice_labels_dt", "title": "nice_labels_dt", "concept": [ "ume data" ], "topics": [ "nice_labels_dt" ] }, { "page": "order_columns", "title": "Order columns", "concept": [ "tools" ], "topics": [ "order_columns" ] }, { "page": "peaklist_demo", "title": "Demo peak list", "concept": [ "ume data" ], "topics": [ "peaklist_demo" ] }, { "page": "remove_blanks", "title": "Remove molecular formulas detected in blanks", "concept": [ "Formula subsetting" ], "topics": [ "remove_blanks" ] }, { "page": "remove_empty_columns", "title": "Remove empty columns", "topics": [ "remove_empty_columns" ] }, { "page": "remove_id_columns", "title": "Remove columns that contain ID's", "concept": [ "Clean data output" ], "topics": [ "remove_id_columns" ] }, { "page": "remove_unknown_columns", "title": "Remove columns that only have one specific value", "concept": [ "Clean data output" ], "topics": [ "remove_unknown_columns" ] }, { "page": "subset_known_mf", "title": "Subsetting known molecular formula categories", "concept": [ "Formula subsetting" ], "topics": [ "subset_known_mf" ] }, { "page": "tab_ume_labels", "title": "Labels of UME columns.", "concept": [ "ume data" ], "topics": [ "tab_ume_labels" ] }, { "page": "theme_uplots", "title": "theme_uplots", "topics": [ "theme_uplots" ] }, { "page": "ume_assign_formulas", "title": "Complete formula assignment (wrapper function)", "concept": [ "Formula assignment", "Formula subsetting", "ume wrapper" ], "topics": [ "ume_assign_formulas" ] }, { "page": "ume_filter_formulas", "title": "Complete Formula subsetting / filtering (wrapper)", "concept": [ "Formula subsetting", "ume wrapper" 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Herzsprung et al. 2014) with Option for Interactive Plot", "concept": [ "uplots" ], "topics": [ "uplot_dbe_vs_o" ] }, { "page": "uplot_freq", "title": "Frequency Plot of a Selected Variable", "topics": [ "uplot_freq" ] }, { "page": "uplot_freq_ma", "title": "Histogram of Mass Accuracy", "concept": [ "uplots" ], "topics": [ "uplot_freq_ma" ] }, { "page": "uplot_freq_vs_ppm", "title": "Mass Accuracy Frequency Histogram", "concept": [ "uplots" ], "topics": [ "uplot_freq_vs_ppm" ] }, { "page": "uplot_hc_vs_m", "title": "H/C vs Molecular Mass Plot", "concept": [ "uplots" ], "topics": [ "uplot_hc_vs_m" ] }, { "page": "uplot_heteroatoms", "title": "Heteroatom Combination vs Mass Accuracy", "concept": [ "uplots" ], "topics": [ "uplot_heteroatoms" ] }, { "page": "uplot_isotope_precision", "title": "Precision of Isotope Abundance", "concept": [ "isotopes", "uplots" ], "topics": [ "uplot_isotope_precision" ] }, { "page": "uplot_kmd", "title": "Kendrick Mass Defect (KMD) vs. Nominal Mass Plot", "concept": [ "uplots" ], "topics": [ "uplot_kmd" ] }, { "page": "uplot_lcms", "title": "Plot LC-MS Spectrum (or fallback MS if no RT available)", "concept": [ "uplots" ], "topics": [ "uplot_lcms" ] }, { "page": "uplot_ma_vs_mz", "title": "Plot Mass Accuracy vs m/z", "concept": [ "uplots" ], "topics": [ "uplot_ma_vs_mz" ] }, { "page": "uplot_ms", "title": "Plot Mass Spectrum", "concept": [ "uplots" ], "topics": [ "uplot_ms" ] }, { "page": "uplot_n_mf_per_sample", "title": "Number of Molecular Formulas per Sample Plot", "concept": [ "uplots" ], "topics": [ "uplot_n_mf_per_sample" ] }, { "page": "uplot_pca", "title": "Plot PCA Results", "concept": [ "uplots" ], "topics": [ "uplot_pca" ] }, { "page": "uplot_ppm_avg", "title": "Plot Median of Mass Accuracy per Sample (ppm)", "topics": [ "uplot_ppm_avg" ] }, { "page": "uplot_ratios", "title": "Molecular Formula Ratio Plot (Sample vs Control)", "concept": [ "uplots" ], "topics": [ "uplot_ratios" ] }, { "page": "uplot_reproducibility", "title": "Check Reproducibility of Sample Analyses", "concept": [ "uplots" ], "topics": [ "uplot_reproducibility" ] }, { "page": "uplot_ri_vs_sample", "title": "Average Relative Intensity per Sample", "concept": [ "uplots" ], "topics": [ "uplot_ri_vs_sample" ] }, { "page": "uplot_vk", "title": "uplot_vk", "concept": [ "uplots" ], "topics": [ "uplot_vk" ] }, { "page": "ustats_outlier", "title": "Outlier detection using multiple statistical tests", "topics": [ "ustats_outlier" ] } ], "_pkglogo": "https://github.com/cran/ume/raw/HEAD/man/figures/logo.png", "_readme": "https://github.com/cran/ume/raw/HEAD/README.md", "_rundeps": [ "askpass", "base64enc", "bslib", "cachem", "cli", "cluster", "cpp11", "crosstalk", "curl", "data.table", "digest", "dplyr", "evaluate", "farver", "fastmap", "fontawesome", "fs", "generics", "ggplot2", "glue", "gridExtra", "gtable", "highr", "htmltools", "htmlwidgets", "httr", "isoband", "jquerylib", "jsonlite", "knitr", "labeling", "later", "lattice", "lazyeval", "lifecycle", "magrittr", "MASS", "Matrix", "memoise", "mgcv", "mime", "nlme", "openssl", "otel", "permute", "pillar", "pkgconfig", "plotly", "promises", "purrr", "R6", "rappdirs", "RColorBrewer", "Rcpp", "rlang", "rmarkdown", "S7", "sass", "scales", "stringi", "stringr", "sys", "tibble", "tidyr", "tidyselect", "tinytex", "utf8", "vctrs", "vegan", "viridis", "viridisLite", "withr", "xfun", "yaml" ], "_vignettes": [ { "source": "ume.Rmd", "filename": "ume.html", "title": "ume", "author": "Boris Koch", "engine": "knitr::rmarkdown", "headings": [ "Getting started", "1. Overview UME data workflow", "All of these tasks can be executed in just two steps:", "Formula assignment and calculation of evaluation parameters", "Formula filtering (subsetting) and normalization", "Alternatively, the workflow can be performed in single steps:", "2. Visualization and statistics", "3. Re-calibration of peaklists", "4. UME core data objects", "Mass Peak List", "Isotopic masses", "Molecular formula library", "Using External UME Formula Libraries", "Create your own molecular formula library", "Molecular formula data", "5. What else can you do with ume?", "Calculate standard parameters", "Converting molecular formulas to a table and vice versa.", "Isotopes", "Create isotope formulas for a parent formula", "Create isotope pattern for a molecular formula", "6. Package content and documentation", "Which version is installed and loaded?", "What is new?", "7. 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