{ "_id": "6a5f872114e95619b75d6802", "Package": "D4TAlink.light", "Type": "Package", "Title": "GDP - Workflow Management", "Version": "2.1.22", "Date": "2026-07-16", "Authors@R": "c(\nperson(given = \"Gregoire\", family = \"Thomas\",\nrole = c(\"aut\", \"cre\", \"cph\"),\nemail = \"gregoire.thomas@SQU4RE.com\",\ncomment = c(ORCID = \"0000-0002-6247-9438\")),\nperson(\"Metabolomic Diagnostics Ltd.\",\nrole = c(\"fnd\"))\n)", "Maintainer": "Gregoire Thomas ", "Description": "Tools, methods and processes for the management of\nanalysis workflows. These lightweight solutions facilitate\nstructuring R&D activities. These solutions were developed to\ncomply with Good Documentation Practice (GDP), with ALCOA+\nprinciples as proposed by the U.S. FDA, and with FAIR\nprinciples as discussed by Jacobsen et al. (2017)\n.", "License": "GPL-3", "Encoding": "UTF-8", "Config/testthat/edition": "3", "VignetteBuilder": "knitr", "URL": "https://bitbucket.org/SQ4/d4talink.light", "ByteCompile": "true", "BugReports": "https://bitbucket.org/SQ4/d4talink.light/issues", "Config/roxygen2/version": "8.0.0", "NeedsCompilation": "no", "Packaged": { "Date": "2026-07-21 14:45:36 UTC", "User": "root" }, "Author": "Gregoire Thomas [aut, cre, cph] (ORCID:\n), Metabolomic\nDiagnostics Ltd. [fnd]", "Config/pak/sysreqs": "cmake libssl-dev", "Repository": "https://cran.r-universe.dev", "Date/Publication": "2026-07-21 14:28:53 UTC", "RemoteUrl": "https://github.com/cran/D4TAlink.light", "RemoteRef": "HEAD", "RemoteSha": "86075017079dc97549dfd0cecae2f24c4e473a24", "_user": "cran", "_type": "src", "_file": "D4TAlink.light_2.1.22.tar.gz", "_fileid": "https://r2.ropensci.org/df8a98e6aa0938b0f7534ca05c8908765ebcc44cb75f9e57887eb98b78fba0ab", "_filesize": 413227, "_sha256": "df8a98e6aa0938b0f7534ca05c8908765ebcc44cb75f9e57887eb98b78fba0ab", "_expires": "2026-10-29T14:50:06.000Z", "_created": "2026-07-21T14:45:36.000Z", "_published": "2026-07-21T14:50:09.089Z", "_jobs": [ { "job": 88668527468, "time": 205, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "8499316132" }, { "job": 88668527525, "time": 202, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "8499314196" }, { "job": 88667377226, "time": 240, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "8499197262" }, { "job": 88668527625, "time": 146, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "8499281882" } ], "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/cran/actions/runs/29840319280", "_status": "success", "_upstream": "https://github.com/cran/D4TAlink.light", "_commit": { "id": "86075017079dc97549dfd0cecae2f24c4e473a24", "author": "Gregoire Thomas ", "committer": "cran-robot ", "message": "version 2.1.22\n", "time": 1784644133 }, "_maintainer": { "name": "Gregoire Thomas", "email": "gregoire.thomas@squ4re.com", "login": "squ4reanalytics", "description": "", "uuid": 122602947, "orcid": "0000-0002-6247-9438" }, "_distro": "resolute", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.1.0", "role": "Depends" }, { "package": "rjson", "role": "Depends" }, { "package": "DBI", "role": "Depends" }, { "package": "RSQLite", "role": "Depends" }, { "package": "openssl", "role": "Depends" }, { "package": "officedown", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "rmarkdown", "role": "Imports" }, { "package": "quarto", "role": "Imports" }, { "package": "Biobase", "role": "Imports" }, { "package": "openxlsx", "role": "Imports" }, { "package": "reticulate", "role": "Imports" }, { "package": "feather", "role": "Imports" }, { "package": "getPass", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "roxygen2", "version": ">= 3.1.0", "role": "Suggests" }, { "package": "WriteXLS", "role": "Suggests" }, { "package": "XLConnect", "role": "Suggests" }, { "package": "xlsx", "role": "Suggests" }, { "package": "testthat", "role": "Suggests" } ], "_owner": "cran", "_selfowned": false, "_usedby": 0, "_updates": [ { "week": "2025-37", "n": 1 }, { "week": "2026-30", "n": 1 } ], "_tags": [ { "name": "2.1.21", "date": "2025-09-11" }, { "name": "2.1.22", "date": "2026-07-21" } ], "_stars": 0, "_contributors": [ { "user": "squ4reanalytics", "count": 10, "uuid": 122602947 } ], "_userbio": { "uuid": 6899542, "type": "organization", "name": "cran", "followers": 622, "description": "Unofficial read-only mirror of all CRAN R packages" }, "_downloads": { "count": 331, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/D4TAlink.light" }, "_devurl": "https://bitbucket.org/sq4/d4talink.light", "_searchresults": 12, "_quarto": true, "_topics": [ "quarto" ], "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/D4TAlink.light.html", "extra/NEWS.html", "extra/NEWS.txt", "manual.pdf" ], "_homeurl": "https://bitbucket.org/sq4/d4talink.light", "_realowner": "squ4reanalytics", "_cranurl": false, "_releases": [ { "version": "2.1.5", "date": "2022-08-26" }, { "version": "2.1.7", "date": "2022-09-05" }, { "version": "2.1.8", "date": "2022-09-15" }, { "version": "2.1.9", "date": "2022-09-16" }, { "version": "2.1.11", "date": "2022-10-22" }, { "version": "2.1.14", "date": "2023-10-04" }, { "version": "2.1.17", "date": "2024-12-02" }, { "version": "2.1.18", "date": "2025-04-02" }, { "version": "2.1.21", "date": "2025-09-11" } ], "_exports": [ "archiveTask", "binaryDir", "binaryFn", "catReport", "datasourceDir", "datasourceFn", "docDir", "docFn", "DTx", "getTaskAuthor", "getTaskEnckey", "getTaskFilepath", "getTaskPaths", "getTaskQmdTemplate", "getTaskRmdTemplate", "getTaskRoot", "getTaskRscriptTemplate", "getTaskSponsor", "getTaskStructure", "initTask", "initTaskQmd", "initTaskRmd", "initTaskRscript", "jpegReport", "jpegReportFn", "listTaskFiles", "listTasks", "loadTask", "pathsDefault", "pathsGLPG", "pathsPMS", "pdfReport", "pdfReportFn", "pngReport", "pngReportFn", "progDir", "qmdFn", "querySQLite", "readBinary", "readFeather", "readPickle", "readReportJSON", "readReportTable", "readSQLite", "renderTaskQmd", "renderTaskRmd", "reportDir", "reportFn", "reportXlsFn", "restoreTask", "rmdFn", "rscriptFn", "saveBinary", "saveBinaryE", "saveFeather", "savePickle", "saveReportJSON", "saveReportTable", "saveReportXls", "saveSQLite", "scanReport", "setTaskAuthor", "setTaskEnckey", "setTaskQmdTemplate", "setTaskRmdTemplate", "setTaskRoot", "setTaskRscriptTemplate", "setTaskSponsor", "setTaskStructure", "taskID" ], "_help": [ { "page": "archiveTask", "title": "Create an archive containing the files of a given task.", "topics": [ "archiveTask" ] }, { "page": "binaryDir", "title": "Get path of binary directory.", "topics": [ "binaryDir" ] }, { "page": "binaryFn", "title": "Get path of binary file.", "topics": [ "binaryFn" ] }, { "page": "catReport", "title": "Output R object using function cat.", "topics": [ "catReport" ] }, { "page": "D4getenv", "title": "Get env var.", "topics": [ "D4getenv" ] }, { "page": "D4TAlink-common-args", "title": "Arguments used across the functions of the D4TAlink package.", "topics": [ "D4TAlink-common-args", "D4TAlink_common_args" ] }, { "page": "D4TAlinkTask", "title": "'D4TAlinkTask' Documentation of the D4TAlinkTask class", "topics": [ "D4TAlinkTask" ] }, { "page": "datasourceDir", "title": "Get path of data source directory.", "topics": [ "datasourceDir" ] }, { "page": "datasourceFn", "title": "Get path of data source file.", "topics": [ "datasourceFn" ] }, { "page": "docDir", "title": "Get path of documentation directory.", "topics": [ "docDir" ] }, { "page": "docFn", "title": "Get path of documentation file.", "topics": [ "docFn" ] }, { "page": "DTx", "title": "Generic function.", "topics": [ "DTx" ] }, { "page": "formatTaskDocx", "title": "Replace default task fields in 'docx' file.", "topics": [ "formatTaskDocx" ] }, { "page": "getTaskAuthor", "title": "Get the name of the task author.", "topics": [ "getTaskAuthor" ] }, { "page": "getTaskEnckey", "title": "Get the encryption key for binary data files.", "topics": [ "getTaskEnckey" ] }, { "page": "getTaskFilepath", "title": "Get the path of a file.", "topics": [ "getTaskFilepath" ] }, { "page": "getTaskPaths", "title": "Get the paths of the task.", "topics": [ "getTaskPaths" ] }, { "page": "getTaskQmdTemplate", "title": "Get the path to the Quarto task template.", "topics": [ "getTaskQmdTemplate" ] }, { "page": "getTaskRmdTemplate", "title": "Get the path to the Rmd task template.", "topics": [ "getTaskRmdTemplate" ] }, { "page": "getTaskRoot", "title": "Get the root of the task repository.", "topics": [ "getTaskRoot" ] }, { "page": "getTaskRscriptTemplate", "title": "Get the path to the R script task template.", "topics": [ "getTaskRscriptTemplate" ] }, { "page": "getTaskSponsor", "title": "Get the name of the task sponsor.", "topics": [ "getTaskSponsor" ] }, { "page": "getTaskStructure", "title": "Get repository directory structure.", "topics": [ "getTaskStructure" ] }, { "page": "initTask", "title": "Initialize a task", "topics": [ "initTask" ] }, { "page": "initTaskQmd", "title": "Create task template in Quarto format.", "topics": [ "initTaskQmd" ] }, { "page": "initTaskRmd", "title": "Create task template in Rmd format.", "topics": [ "initTaskRmd" ] }, { "page": "initTaskRscript", "title": "Create task R script.", "topics": [ "initTaskRscript" ] }, { "page": "jpegReport", "title": "Graphics devices for 'JPEG' format bitmap files.", "topics": [ "jpegReport" ] }, { "page": "jpegReportFn", "title": "Get path of 'jpeg' output file.", "topics": [ "jpegReportFn" ] }, { "page": "listTaskFiles", "title": "List the files associated to a task.", "topics": [ "listTaskFiles" ] }, { "page": "listTasks", "title": "List details of all tasks stored in the root directory.", "topics": [ "listTasks" ] }, { "page": "loadTask", "title": "Load a task.", "topics": [ "loadTask" ] }, { "page": "pathsDefault", "title": "Task paths generator.", "topics": [ "pathsDefault" ] }, { "page": "pathsGLPG", "title": "Task paths generator.", "topics": [ "pathsGLPG" ] }, { "page": "pathsPMS", "title": "Task paths generator.", "topics": [ "pathsPMS" ] }, { "page": "pdfReport", "title": "Graphics devices for 'pdf' format bitmap files.", "topics": [ "pdfReport" ] }, { "page": "pdfReportFn", "title": "Get path of 'pdf' output file.", "topics": [ "pdfReportFn" ] }, { "page": "pngReport", "title": "Graphics devices for 'PNG' format bitmap files.", "topics": [ "pngReport" ] }, { "page": "pngReportFn", "title": "Get path of 'png' output file.", "topics": [ "pngReportFn" ] }, { "page": "progDir", "title": "Get path of scripts directory.", "topics": [ "progDir" ] }, { "page": "qmdFn", "title": "Get path of R script file name.", "topics": [ "qmdFn" ] }, { "page": "querySQLite", "title": "Load data frame by querying an SQLite database. This function executes a SQL query on an SQLite database file created with 'saveSQLite'.", "topics": [ "querySQLite" ] }, { "page": "readBinary", "title": "Restore R object from binary file.", "topics": [ "readBinary" ] }, { "page": "readFeather", "title": "Restore R data.frame from Apache Arrow feather file.", "topics": [ "readFeather" ] }, { "page": "readPickle", "title": "Restore R data.frame from a Python pickle file.", "topics": [ "readPickle" ] }, { "page": "readReportJSON", "title": "Read JSON data into R object.", "topics": [ "readReportJSON" ] }, { "page": "readReportTable", "title": "Read data into vector or list using function 'scan'.", "topics": [ "readReportTable" ] }, { "page": "readSQLite", "title": "Load data frame from SQLite. This function reads a data frame from an SQLite database file created with 'saveSQLite'.", "topics": [ "readSQLite" ] }, { "page": "renderTaskQmd", "title": "Render the task from the Qmd file", "topics": [ "renderTaskQmd" ] }, { "page": "renderTaskRmd", "title": "Render the task from the Rmd file", "topics": [ "renderTaskRmd" ] }, { "page": "reportDir", "title": "Get path of report directory.", "topics": [ "reportDir" ] }, { "page": "reportFn", "title": "Get path of output file.", "topics": [ "reportFn" ] }, { "page": "reportXlsFn", "title": "Get path of 'xlsx' output file.", "topics": [ "reportXlsFn" ] }, { "page": "restoreTask", "title": "Restore an archive containing the files of a given task from a file created with archiveTask.", "topics": [ "restoreTask" ] }, { "page": "rmdFn", "title": "Get path of R script file name.", "topics": [ "rmdFn" ] }, { "page": "rscriptFn", "title": "Get path of R script file name.", "topics": [ "rscriptFn" ] }, { "page": "saveBinary", "title": "Save R object in binary file.", "topics": [ "saveBinary" ] }, { "page": "saveBinaryE", "title": "Save R object in encrypted binary file.", "topics": [ "saveBinaryE" ] }, { "page": "saveFeather", "title": "Save R object in Apache Arrow feather file.", "topics": [ "saveFeather" ] }, { "page": "savePickle", "title": "Save R object in Python pickle file.", "topics": [ "savePickle" ] }, { "page": "saveReportJSON", "title": "Output R object in JSON format.", "topics": [ "saveReportJSON" ] }, { "page": "saveReportTable", "title": "Output R object using function 'write.csv'.", "topics": [ "saveReportTable" ] }, { "page": "saveReportXls", "title": "Save R object in binary file.", "topics": [ "saveReportXls" ] }, { "page": "saveSQLite", "title": "Save R data frame to SQLite file. This function saves a data frame to an SQLite database file. It can create indices on specified columns for faster querying. The database file is stored in the task's binary directory.", "topics": [ "saveSQLite" ] }, { "page": "scanReport", "title": "Read data into vector or list using function 'scan'.", "topics": [ "scanReport" ] }, { "page": "setTaskAuthor", "title": "Set the name of the tasks author.", "topics": [ "setTaskAuthor" ] }, { "page": "setTaskEnckey", "title": "Set the encryption key for binary data files.", "topics": [ "setTaskEnckey" ] }, { "page": "setTaskQmdTemplate", "title": "Set the path to the Quarto task template.", "topics": [ "setTaskQmdTemplate" ] }, { "page": "setTaskRmdTemplate", "title": "Set the path to the Rmd task template.", "topics": [ "setTaskRmdTemplate" ] }, { "page": "setTaskRoot", "title": "Set the root of the task repository.", "topics": [ "setTaskRoot" ] }, { "page": "setTaskRscriptTemplate", "title": "Set the path to the R script task template.", "topics": [ "setTaskRscriptTemplate" ] }, { "page": "setTaskSponsor", "title": "Set the name of the tasks sponsor.", "topics": [ "setTaskSponsor" ] }, { "page": "setTaskStructure", "title": "Set task repository directory structure.", "topics": [ "setTaskStructure" ] }, { "page": "taskID", "title": "Get task identifier string.", "topics": [ "taskID" ] } ], "_rundeps": [ "arrow", "askpass", "assertthat", "base64enc", "Biobase", "BiocGenerics", "bit", "bit64", "blob", "bslib", "cachem", "cli", "cpp11", "DBI", "digest", "dplyr", "evaluate", "fastmap", "feather", "fontawesome", "fontBitstreamVera", "fontLiberation", "fontquiver", "fs", "gdtools", "generics", "getPass", "glue", "here", "highr", "htmltools", "jquerylib", "jsonlite", "knitr", "later", "lattice", "lifecycle", "magrittr", "Matrix", "memoise", "mime", "officedown", "officer", "openssl", "openxlsx", "pillar", "pkgconfig", "png", "processx", "ps", "purrr", "quarto", "R6", "ragg", "rappdirs", "Rcpp", "RcppTOML", "reticulate", "rjson", "rlang", "rmarkdown", "rprojroot", "RSQLite", "rstudioapi", "rvg", "sass", "stringi", "stringr", "sys", "systemfonts", "textshaping", "tibble", "tidyr", "tidyselect", "tinytex", "utf8", "uuid", "vctrs", "withr", "xfun", "xml2", "yaml", "zip" ], "_vignettes": [ { "source": "D4TAlink_basics.Rmd", "filename": "D4TAlink_basics.html", "title": "D4TAlink.light - Manual", "author": "Grégoire Thomas", "engine": "knitr::rmarkdown", "headings": [ "1. Introduction", "2. Installation", "3. Quick start", "4. Usage", "4.1. Parametrisation", "4.2. Analysis task", "4.3. Task content", "4.4. Create and render an R markdown file", "4.5. Create an R script", "4.6. Report data", "4.7. Transfer data between tasks", "4.8. Share a task", "4.9. R markdown and script templates", "4.10. Change directory structure" ], "created": "2022-08-26 06:52:41", "modified": "2024-12-02 10:00:26", "commits": 7 }, { "source": "D4TAlink_quickstart.Rmd", "filename": "D4TAlink_quickstart.html", "title": "D4TAlink.light - Quick start", "author": "Grégoire Thomas", "engine": "knitr::rmarkdown", "headings": [], "created": "2022-10-22 09:07:50", "modified": "2024-12-02 10:00:26", "commits": 3 } ], "_score": 2.6812412373755876, "_indexed": false, "_nocasepkg": "d4talink.light", "_universes": [ "cran" ], "_indexurl": "https://squ4reanalytics.r-universe.dev/D4TAlink.light", "_previous": "2.1.21", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "2.1.22", "date": "2026-07-21T14:48:23.000Z", "distro": "resolute", "commit": "86075017079dc97549dfd0cecae2f24c4e473a24", "fileid": "https://r2.ropensci.org/c2266231e101e16d401a3be1f0f70823f21090720c6fcb3b8ad54ef0fb8a7705", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/29840319280" }, { "r": "4.6.1", "os": "linux", "version": "2.1.22", "date": "2026-07-21T14:48:20.000Z", "distro": "resolute", "commit": "86075017079dc97549dfd0cecae2f24c4e473a24", "fileid": "https://r2.ropensci.org/349d3ebd04c5578e313f74a73f45b4825c2638218ec7372981c16a067b24888d", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/29840319280" }, { "r": "4.6.0", "os": "wasm", "version": "2.1.22", "date": "2026-07-21T14:48:30.000Z", "commit": "86075017079dc97549dfd0cecae2f24c4e473a24", "fileid": "https://r2.ropensci.org/f9f40fd76eb243de1517d6175a0978ddec2af312fc16bd1c237a0d172d86bd03", "status": "success", "buildurl": "https://github.com/r-universe/cran/actions/runs/29840319280" } ] }