diff --git a/.Rbuildignore b/.Rbuildignore index 74cb3a131290bdbfe13fb4d2a37a5e1b70261c75..6ccd837a666851dff41fdf78a59a36f45e5570a4 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -1,3 +1,5 @@ +^renv$ +^renv\.lock$ ^.*\.Rproj$ ^\.Rproj\.user$ ^data-raw$ diff --git a/.Rprofile b/.Rprofile new file mode 100644 index 0000000000000000000000000000000000000000..81b960f5c6a8ee40840badd620f8af9743787730 --- /dev/null +++ b/.Rprofile @@ -0,0 +1 @@ +source("renv/activate.R") diff --git a/.gitignore b/.gitignore index 34134b0d4f27cbf751051ec41b6b01a9f9d0fa42..5aab0068a6dd7a9e08402e74fdc39cbc12a463bf 100644 --- a/.gitignore +++ b/.gitignore @@ -9,6 +9,6 @@ /.project .settings /.dbeaver/ -*/tempplot +# */tempplot inst/doc *.log diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml index f5298c73903a289af1b5ca18388e16921f828eac..8787f7ecbe19de37d9df6948841999a886cdf165 100644 --- a/.gitlab-ci.yml +++ b/.gitlab-ci.yml @@ -1,64 +1,57 @@ -# test config -image: rocker/tidyverse - stages: # List of stages for jobs, and their order of execution + - testdb - build - document - check - covr - + - build_images + - deploy + variables: - R_LIBS_USER: "$CI_PROJECT_DIR/ci/lib" + PG_USER: stacomi_test + PG_USER_PASSWORD: stacomi_test + PG_DB: bd_contmig_nat + PG_HOST: host_db + PG_PORT: 5432 + POSTGRES_PASSWORD: postgres + stacomi_db_path: $CI_REGISTRY/stacomi/$db_image_name + db_image_name: "stacomi_db" + db_version: "0.6.0" + postgres_version: "17" + postgis_version: "3.5" + db_image_tagdev: "$db_version-pg$postgres_version-ps$postgis_version" + RENV_PATHS_CACHE: "renv/cache" + RENV_PATHS_LIBRARY: "renv/library" + # R_LIBS_USER: "$CI_PROJECT_DIR/ci/lib" CHECK_DIR: "$CI_PROJECT_DIR/ci/logs" BUILD_DIR: "$CI_PROJECT_DIR/ci/build" BUILD_LOGS_DIR: "$CI_PROJECT_DIR/ci/logs/$CI_PROJECT_NAME.Rcheck" + r_image_dev: rocker/shiny-verse:latest + r_image: rocker/shiny-verse:latest + docker_version: "20.10" -# the .Renviron in the document folder contains the path to the libraries in the form R_LIBS=$CI_PROJECT_DIR/ci/lib -# there are three lines added there so the uploaded packages will end up there -before_script: - - apt-get update - - apt-get install -y qpdf - - mkdir -p $R_LIBS_USER $BUILD_LOGS_DIR $BUILD_DIR - - echo 'R_LIBS=$R_LIBS_USER' > .Renviron - - echo 'R_LIBS_USER=$R_LIBS_USER' >> .Renviron - - echo 'R_LIBS_SITE=$R_LIBS_USER' >> .Renviron - -# below CI_COMMIT_REF_SLUG is CI_COMMIT_REF_NAME The branch or tag name for which project is built, in lowercase, shortened to 63 bytes -buildbinary: - stage: build - script: - # dependencies =TRUE only supports one - - R -e 'install.packages(pkgs=c("testthat"), dependencies = TRUE, repos ="https://pbil.univ-lyon1.fr/CRAN/")' - - R -e 'install.packages(pkgs=c("devtools"), dependencies = TRUE, repos ="https://pbil.univ-lyon1.fr/CRAN/")' - # below TRUE is shorthand for "Depends", "Imports", "LinkingTo" and "Suggests". - - R -e 'devtools::install_deps(dependencies = TRUE, lib = Sys.getenv("R_LIBS_USER"))' - - R -e 'devtools::build(binary = TRUE, path=Sys.getenv("BUILD_DIR"), vignettes=FALSE, manual=FALSE)' - cache: - key: "$CI_COMMIT_REF_SLUG" - paths: - - "$R_LIBS_USER" - artifacts: - paths: - - "$BUILD_DIR" +#key for caching per branch +cache: + key: $CI_COMMIT_REF_SLUG + paths: + - ${RENV_PATHS_CACHE} + - ${RENV_PATHS_LIBRARY} + # - ${R_LIBS_USER} -documentation: - stage: document - script: - - R -e 'devtools::document()' - -checkerrors: - stage: check - script: - - R -e 'devtools::check(check_dir = Sys.getenv("CHECK_DIR"), document = FALSE, args = "--no-tests")' - - R -e 'if (length(devtools::check_failures(path = Sys.getenv("BUILD_LOGS_DIR"), note = FALSE)) > 0) stop()' - cache: - paths: - - $R_LIBS_USER - coverage: stage: covr + extends: + - .rules_shut_down script: - - R -e 'install.packages(pkgs=c("covr"), dependencies = TRUE, repos ="https://pbil.univ-lyon1.fr/CRAN/")' - - R -e 'covr::package_coverage(Sys.getenv("CI_PROJECT_DIR"))' + - R -e 'install.packages(pkgs=c("covr"), dependencies = TRUE, repos ="https://pbil.univ-lyon1.fr/CRAN/")' + - R -e 'covr::package_coverage(Sys.getenv("CI_PROJECT_DIR"))' - \ No newline at end of file +include: + - local: "/gitlab-ci/rules.gitlab-ci.yml" # generic rules to be used for main branch or others + - local: "/gitlab-ci/image.gitlab-ci.yml" # image to be used for main branch or others + - local: "/gitlab-ci/service.gitlab-ci.yml" # stacomi db + - local: '/gitlab-ci/testdb.gitlab-ci.yml' + - local: "/gitlab-ci/build_binary.gitlab-ci.yml" + - local: '/gitlab-ci/pkgdown.gitlab-ci.yml' + - local: "/gitlab-ci/check.gitlab-ci.yml" + - local: "/gitlab-ci/build_images_docker.gitlab-ci.yml" # building docker images diff --git a/DESCRIPTION b/DESCRIPTION index 1849444b6f036e00113fa415f94889c5e7493518..5006b4bb41592d25c8612b4c525b59791a4f264c 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -11,6 +11,7 @@ Imports: processx, attempt, DT, + ggthemes, glue, htmltools, stacomirtools (>= 0.6.1.0), @@ -39,9 +40,6 @@ Suggests: Language: en-US URL: https://forgemia.inra.fr/stacomi/stacoshiny BugReports: https://forgemia.inra.fr/stacomi/stacoshiny/issues -Remotes: - git::https://forgemia.inra.fr/stacomi/stacomirtools.git, - git::https://forgemia.inra.fr/stacomi/stacomir.git VignetteBuilder: knitr Depends: R (>= 2.10) diff --git a/R/global.R b/R/global.R index 4698ed7ee0a700f4ee24464b383efd95cc92a0d4..b532634034f0bbc369f454beb89ff90a6241c09b 100644 --- a/R/global.R +++ b/R/global.R @@ -2,13 +2,17 @@ # current year, for the UI CY <- as.numeric(strftime(Sys.time(), format = "%Y")) -dir.create(normalizePath("./data/tempplot"),showWarnings = FALSE) +dir.create( + normalizePath("./data/tempplot"), + showWarnings = FALSE, + recursive = TRUE +) options( stacomiR.dbname = "bd_contmig_nat", - stacomiR.host = "localhost", + stacomiR.host = "host_db", stacomiR.port = "5432", - stacomiR.user = "postgres", - stacomiR.password = "postgres" + stacomiR.user = "stacomi_test", + stacomiR.password = "stacomi_test" ) library(stacomiR) library(magrittr) diff --git a/data/tempplot/.gitkeep b/data/tempplot/.gitkeep new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/gitlab-ci/build_binary.gitlab-ci.yml b/gitlab-ci/build_binary.gitlab-ci.yml new file mode 100644 index 0000000000000000000000000000000000000000..10abcff605a933a04d03aecbbbad86f666827499 --- /dev/null +++ b/gitlab-ci/build_binary.gitlab-ci.yml @@ -0,0 +1,46 @@ +.buildpackage: + stage: build + extends: + - .image-dev + script: + - apt-get update && apt-get install -y git + # - mkdir -p $R_LIBS_USER + - mkdir -p $RENV_PATHS_LIBRARY + - mkdir -p $RENV_PATHS_CACHE + - mkdir -p public + - echo "install packages" + - | + Rscript -e ' + source("renv/activate.R"); + if(!requireNamespace("pak", quietly = TRUE)) {install.packages("pak", lib = "'${RENV_PATHS_LIBRARY}'")}; + pak::pkg_install(pkg = c("rcmdcheck", "renv", "devtools"), upgrade = FALSE, lib = "'${RENV_PATHS_LIBRARY}'"); + renv::restore(library = "'${RENV_PATHS_LIBRARY}'"); + devtools::build(binary = TRUE, path="public", vignettes=TRUE, manual=TRUE); + devtools::build(binary = FALSE, path="public", vignettes=TRUE) + ' + + artifacts: + when: always + paths: + - public + # - ${R_LIBS_USER} + +# en dev +buildpackage-dev: + needs: + - test_db-dev + extends: + - .rules_other + - .buildpackage + - .image-dev + - .service-dev + +# en prod +buildpackage-prod: + needs: + - test_db-prod + extends: + - .rules_main + - .buildpackage + - .image-prod + - .service-prod diff --git a/gitlab-ci/build_images_docker.gitlab-ci.yml b/gitlab-ci/build_images_docker.gitlab-ci.yml new file mode 100644 index 0000000000000000000000000000000000000000..f34dc684954e58bcd00e332c138bfb5367b2e015 --- /dev/null +++ b/gitlab-ci/build_images_docker.gitlab-ci.yml @@ -0,0 +1,32 @@ +# build docker images + +####################### +# for any branch, but main +build_stacoshiny-dev: + image: docker:$docker_version + stage: build_images + services: + - docker:$docker_version_dind + extends: + - .rules_shut_down + script: + - echo $CI_REGISTRY_PASSWORD | docker login -u $CI_REGISTRY_USER $CI_REGISTRY --password-stdin + - docker build -t $CI_REGISTRY_IMAGE/${stacoshiny_image_name}:${stacoshiny_version}-$tag_dev -f stacoshiny.dockerfile . + - docker push --all-tags $CI_REGISTRY_IMAGE/${stacoshiny_image_name} + +####################### +# for main banch only +build_stacoshiny-prod: + image: docker:$docker_version + stage: build_images + services: + - docker:$docker_version_dind + extends: + - .rules_shut_down + when: manual + script: + - echo $CI_REGISTRY_PASSWORD | docker login -u $CI_REGISTRY_USER $CI_REGISTRY --password-stdin + - docker build -t $CI_REGISTRY_IMAGE/${stacoshiny_image_name}:${stacoshiny_version} -f stacoshiny.dockerfile . + - docker tag $CI_REGISTRY_IMAGE/${stacoshiny_image_name}:${stacoshiny_version} $CI_REGISTRY_IMAGE/${stacoshiny_image_name}:latest + - docker push --all-tags $CI_REGISTRY_IMAGE/${stacoshiny_image_name} + \ No newline at end of file diff --git a/gitlab-ci/check.gitlab-ci.yml b/gitlab-ci/check.gitlab-ci.yml new file mode 100644 index 0000000000000000000000000000000000000000..3965a7e35bb4e39de22bd2b9555bc038e0a84d33 --- /dev/null +++ b/gitlab-ci/check.gitlab-ci.yml @@ -0,0 +1,39 @@ +# https://cran.r-project.org/web/packages/littler/vignettes/littler-examples.html +.checkerrors: + before_script: + - apt-get update + - apt-get install -y qpdf + stage: check + script: + - mkdir -p public/check + - | + r -e ' + Sys.setenv("_R_CHECK_SYSTEM_CLOCK_" = 0); + source("renv/activate.R"); + renv::restore(library = "'${RENV_PATHS_LIBRARY}'"); + devtools::load_all(); + devtools::check(document = FALSE, args = "--no-tests", check_dir="public/check") + ' + artifacts: + when: always + paths: + - public/check + expire_in: 30 days + +# en dev +checkerrors-dev: + extends: + - .rules_other + - .checkerrors + - .image-dev + - .service-dev + needs: ["buildpackage-dev"] + +# en prod +checkerrors-prod: + extends: + - .rules_main + - .checkerrors + - .image-prod + - .service-prod + needs: ["buildpackage-prod"] diff --git a/gitlab-ci/image.gitlab-ci.yml b/gitlab-ci/image.gitlab-ci.yml new file mode 100644 index 0000000000000000000000000000000000000000..f56b3cfddcdd417fe3b47cd88f601de6dc45aa54 --- /dev/null +++ b/gitlab-ci/image.gitlab-ci.yml @@ -0,0 +1,10 @@ +# to use the right docker db image + +####################### +# for any branch, but main +.image-dev: + image: ${CI_DEPENDENCY_PROXY_DIRECT_GROUP_IMAGE_PREFIX}/${r_image_dev} +####################### +# for main branch only +.image-prod: + image: ${CI_DEPENDENCY_PROXY_DIRECT_GROUP_IMAGE_PREFIX}/${r_image} \ No newline at end of file diff --git a/gitlab-ci/pkgdown.gitlab-ci.yml b/gitlab-ci/pkgdown.gitlab-ci.yml new file mode 100644 index 0000000000000000000000000000000000000000..32c09b1fd28472262c48633b311df8b044dbd8dd --- /dev/null +++ b/gitlab-ci/pkgdown.gitlab-ci.yml @@ -0,0 +1,40 @@ +.pkgdown: + stage: document + allow_failure: true + when: on_success + script: + - mkdir -p public/documentation + - | + Rscript -e ' + source("renv/activate.R"); + if(!requireNamespace("pak", quietly = TRUE)) {install.packages("pak", lib = "'${RENV_PATHS_LIBRARY}'")}; + pak::pkg_install(pkg = c("rcmdcheck", "renv", "devtools"), upgrade = FALSE, lib = "'${RENV_PATHS_LIBRARY}'"); + renv::restore(library = "'${RENV_PATHS_LIBRARY}'"); + pak::pkg_install(pkg = c("pkgdown"), upgrade = FALSE, lib = "'${RENV_PATHS_LIBRARY}'"); + pak::pak(pkg = ".", upgrade = FALSE, lib = "'${RENV_PATHS_LIBRARY}'")'; + devtools::document(); + pkgdown::build_site() + ' + - cp -r docs/* public + artifacts: + paths: + - public + expire_in: 30 days + +# en dev +pkgdown-dev: + extends: + - .rules_other + - .pkgdown + - .image-dev + - .service-dev + needs: ["buildpackage-dev"] + +# en prod +pkgdown-prod: + extends: + - .rules_main + - .pkgdown + - .image-prod + - .service-prod + needs: ["buildpackage-prod"] \ No newline at end of file diff --git a/gitlab-ci/publication.gitlab-ci.yml b/gitlab-ci/publication.gitlab-ci.yml new file mode 100644 index 0000000000000000000000000000000000000000..14621dcf45f3a3a3b410b0a8fd4f8f6ccf441a1c --- /dev/null +++ b/gitlab-ci/publication.gitlab-ci.yml @@ -0,0 +1,45 @@ +.publication: + stage: deploy + allow_failure: true + when: on_success + script: + - echo "publication" + artifacts: + paths: + - public + expire_in: 30 days + +# en dev +publication-dev: + extends: + - .rules_other + - .publication + - .image-dev + needs: ["pkgdown-dev"] + environment: + name: $CI_COMMIT_REF_SLUG + url: https://$CI_PROJECT_NAMESPACE.$CI_PAGES_DOMAIN/-/$CI_PROJECT_NAME/-/jobs/$CI_JOB_ID/artifacts/public/index.html + on_stop: stop-pkgdown-dev + +stop-pkgdown-dev: + stage: deploy + extends: + - .rules_other + script: + - echo "Supprime l'environnement de test" + environment: + name: $CI_COMMIT_REF_SLUG + action: stop + when: manual + +# en prod +pages: + extends: + - .rules_main + stage: deploy + script: + - echo "deployment" + artifacts: + paths: + - public + needs: ["pkgdown-prod"] \ No newline at end of file diff --git a/gitlab-ci/rules.gitlab-ci.yml b/gitlab-ci/rules.gitlab-ci.yml new file mode 100644 index 0000000000000000000000000000000000000000..1294670549d96221d49fdd834b85f621ef27f67d --- /dev/null +++ b/gitlab-ci/rules.gitlab-ci.yml @@ -0,0 +1,19 @@ +# generic rules to be used for main branch or others + +####################### +# for any branch, but main +.rules_other: + rules: + - if: $CI_COMMIT_BRANCH != $CI_DEFAULT_BRANCH && $CI_COMMIT_BRANCH != "main" && $CI_COMMIT_REF_PROTECTED != "true" # only if there is changes in branch other than main + +####################### +# for main banch only +.rules_main: + rules: + - if: $CI_COMMIT_BRANCH == $CI_DEFAULT_BRANCH || $CI_COMMIT_BRANCH == "main" || $CI_COMMIT_REF_PROTECTED == "true" # only if there is changes in the main branch + +####################### +# for shutting down the job +.rules_shut_down: + rules: + - when: never \ No newline at end of file diff --git a/gitlab-ci/service.gitlab-ci.yml b/gitlab-ci/service.gitlab-ci.yml new file mode 100644 index 0000000000000000000000000000000000000000..334c08db8e8a2da7727082a8d6edc4886612aef2 --- /dev/null +++ b/gitlab-ci/service.gitlab-ci.yml @@ -0,0 +1,10 @@ +.service-dev: + services: + - name: ${stacomi_db_path}/${db_image_name}:${db_image_tagdev} + alias: $PG_HOST + + +.service-prod: + services: + - name: ${stacomi_db_path}/${db_image_name}:latest + alias: $PG_HOST diff --git a/gitlab-ci/testdb.gitlab-ci.yml b/gitlab-ci/testdb.gitlab-ci.yml new file mode 100644 index 0000000000000000000000000000000000000000..19aada41bc3b57105cdb9a4c38440ea0cc7b0f10 --- /dev/null +++ b/gitlab-ci/testdb.gitlab-ci.yml @@ -0,0 +1,28 @@ +.test_db: + stage: testdb + image: ${CI_DEPENDENCY_PROXY_DIRECT_GROUP_IMAGE_PREFIX}/postgres:${postgres_version} + before_script: + - echo "En attente de la disponibilité de PostgreSQL" + - | + until pg_isready -U $PG_USER -h $PG_HOST -p $PG_PORT -d $PG_DB; do + sleep 2 + done + - psql --version + - export PGPASSWORD=$PG_USER_PASSWORD + script: + - psql -U $PG_USER -h $PG_HOST -p $PG_PORT -d $PG_DB -c "SELECT version();" + - psql -U $PG_USER -h $PG_HOST -p $PG_PORT -d $PG_DB -c "SELECT * from test.t_dispositifcomptage_dic" + +# en dev +test_db-dev: + extends: + - .rules_other + - .test_db + - .service-dev + +# en prod +test_db-prod: + extends: + - .rules_main + - .test_db + - .service-prod \ No newline at end of file diff --git a/renv.lock b/renv.lock new file mode 100644 index 0000000000000000000000000000000000000000..9bc3f14da0f66884c9f65e6897508d99f182395f --- /dev/null +++ b/renv.lock @@ -0,0 +1,4998 @@ +{ + "R": { + "Version": "4.4.2", + "Repositories": [ + { + "Name": "CRAN", + "URL": "https://cloud.r-project.org" + } + ] + }, + "Packages": { + "DBI": { + "Package": "DBI", + "Version": "1.2.3", + "Source": "Repository", + "Title": "R Database Interface", + "Date": "2024-06-02", + "Authors@R": "c( person(\"R Special Interest Group on Databases (R-SIG-DB)\", role = \"aut\"), person(\"Hadley\", \"Wickham\", role = \"aut\"), person(\"Kirill\", \"Müller\", , \"kirill@cynkra.com\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-1416-3412\")), person(\"R Consortium\", role = \"fnd\") )", + "Description": "A database interface definition for communication between R and relational database management systems. All classes in this package are virtual and need to be extended by the various R/DBMS implementations.", + "License": "LGPL (>= 2.1)", + "URL": "https://dbi.r-dbi.org, https://github.com/r-dbi/DBI", + "BugReports": "https://github.com/r-dbi/DBI/issues", + "Depends": [ + "methods", + "R (>= 3.0.0)" + ], + "Suggests": [ + "arrow", + "blob", + "covr", + "DBItest", + "dbplyr", + "downlit", + "dplyr", + "glue", + "hms", + "knitr", + "magrittr", + "nanoarrow (>= 0.3.0.1)", + "RMariaDB", + "rmarkdown", + "rprojroot", + "RSQLite (>= 1.1-2)", + "testthat (>= 3.0.0)", + "vctrs", + "xml2" + ], + "VignetteBuilder": "knitr", + "Config/autostyle/scope": "line_breaks", + "Config/autostyle/strict": "false", + "Config/Needs/check": "r-dbi/DBItest", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.1", + "Config/Needs/website": "r-dbi/DBItest, r-dbi/dbitemplate, adbi, AzureKusto, bigrquery, DatabaseConnector, dittodb, duckdb, implyr, lazysf, odbc, pool, RAthena, IMSMWU/RClickhouse, RH2, RJDBC, RMariaDB, RMySQL, RPostgres, RPostgreSQL, RPresto, RSQLite, sergeant, sparklyr, withr", + "Config/testthat/edition": "3", + "NeedsCompilation": "no", + "Author": "R Special Interest Group on Databases (R-SIG-DB) [aut], Hadley Wickham [aut], Kirill Müller [aut, cre] (<https://orcid.org/0000-0002-1416-3412>), R Consortium [fnd]", + "Maintainer": "Kirill Müller <kirill@cynkra.com>", + "Repository": "CRAN" + }, + "DT": { + "Package": "DT", + "Version": "0.33", + "Source": "Repository", + "Type": "Package", + "Title": "A Wrapper of the JavaScript Library 'DataTables'", + "Authors@R": "c( person(\"Yihui\", \"Xie\", role = \"aut\"), person(\"Joe\", \"Cheng\", email = \"joe@posit.co\", role = c(\"aut\", \"cre\")), person(\"Xianying\", \"Tan\", role = \"aut\"), person(\"JJ\", \"Allaire\", role = \"ctb\"), person(\"Maximilian\", \"Girlich\", role = \"ctb\"), person(\"Greg\", \"Freedman Ellis\", role = \"ctb\"), person(\"Johannes\", \"Rauh\", role = \"ctb\"), person(\"SpryMedia Limited\", role = c(\"ctb\", \"cph\"), comment = \"DataTables in htmlwidgets/lib\"), person(\"Brian\", \"Reavis\", role = c(\"ctb\", \"cph\"), comment = \"selectize.js in htmlwidgets/lib\"), person(\"Leon\", \"Gersen\", role = c(\"ctb\", \"cph\"), comment = \"noUiSlider in htmlwidgets/lib\"), person(\"Bartek\", \"Szopka\", role = c(\"ctb\", \"cph\"), comment = \"jquery.highlight.js in htmlwidgets/lib\"), person(\"Alex\", \"Pickering\", role = c(\"ctb\")), person(\"William\", \"Holmes\", role = c(\"ctb\")), person(\"Mikko\", \"Marttila\", role = c(\"ctb\")), person(\"Andres\", \"Quintero\", role = c(\"ctb\")), person(\"Stéphane\", \"Laurent\", role = c(\"ctb\")), person(given = \"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", + "Description": "Data objects in R can be rendered as HTML tables using the JavaScript library 'DataTables' (typically via R Markdown or Shiny). The 'DataTables' library has been included in this R package. The package name 'DT' is an abbreviation of 'DataTables'.", + "URL": "https://github.com/rstudio/DT", + "BugReports": "https://github.com/rstudio/DT/issues", + "License": "GPL-3 | file LICENSE", + "Imports": [ + "htmltools (>= 0.3.6)", + "htmlwidgets (>= 1.3)", + "httpuv", + "jsonlite (>= 0.9.16)", + "magrittr", + "crosstalk", + "jquerylib", + "promises" + ], + "Suggests": [ + "knitr (>= 1.8)", + "rmarkdown", + "shiny (>= 1.6)", + "bslib", + "future", + "testit", + "tibble" + ], + "VignetteBuilder": "knitr", + "RoxygenNote": "7.3.1", + "Encoding": "UTF-8", + "NeedsCompilation": "no", + "Author": "Yihui Xie [aut], Joe Cheng [aut, cre], Xianying Tan [aut], JJ Allaire [ctb], Maximilian Girlich [ctb], Greg Freedman Ellis [ctb], Johannes Rauh [ctb], SpryMedia Limited [ctb, cph] (DataTables in htmlwidgets/lib), Brian Reavis [ctb, cph] (selectize.js in htmlwidgets/lib), Leon Gersen [ctb, cph] (noUiSlider in htmlwidgets/lib), Bartek Szopka [ctb, cph] (jquery.highlight.js in htmlwidgets/lib), Alex Pickering [ctb], William Holmes [ctb], Mikko Marttila [ctb], Andres Quintero [ctb], Stéphane Laurent [ctb], Posit Software, PBC [cph, fnd]", + "Maintainer": "Joe Cheng <joe@posit.co>", + "Repository": "CRAN" + }, + "Formula": { + "Package": "Formula", + "Version": "1.2-5", + "Source": "Repository", + "Date": "2023-02-23", + "Title": "Extended Model Formulas", + "Description": "Infrastructure for extended formulas with multiple parts on the right-hand side and/or multiple responses on the left-hand side (see <doi:10.18637/jss.v034.i01>).", + "Authors@R": "c(person(given = \"Achim\", family = \"Zeileis\", role = c(\"aut\", \"cre\"), email = \"Achim.Zeileis@R-project.org\", comment = c(ORCID = \"0000-0003-0918-3766\")), person(given = \"Yves\", family = \"Croissant\", role = \"aut\", email = \"Yves.Croissant@univ-reunion.fr\"))", + "Depends": [ + "R (>= 2.0.0)", + "stats" + ], + "License": "GPL-2 | GPL-3", + "NeedsCompilation": "no", + "Author": "Achim Zeileis [aut, cre] 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It also contains a number of lower level 'CLI' elements: rules, boxes, trees, and 'Unicode' symbols with 'ASCII' alternatives. It support ANSI colors and text styles as well.", + "License": "MIT + file LICENSE", + "URL": "https://cli.r-lib.org, https://github.com/r-lib/cli", + "BugReports": "https://github.com/r-lib/cli/issues", + "Depends": [ + "R (>= 3.4)" + ], + "Imports": [ + "utils" + ], + "Suggests": [ + "callr", + "covr", + "crayon", + "digest", + "glue (>= 1.6.0)", + "grDevices", + "htmltools", + "htmlwidgets", + "knitr", + "methods", + "processx", + "ps (>= 1.3.4.9000)", + "rlang (>= 1.0.2.9003)", + "rmarkdown", + "rprojroot", + "rstudioapi", + "testthat (>= 3.2.0)", + "tibble", + "whoami", + "withr" + ], + "Config/Needs/website": "r-lib/asciicast, bench, brio, cpp11, decor, desc, fansi, prettyunits, sessioninfo, tidyverse/tidytemplate, usethis, vctrs", + "Config/testthat/edition": "3", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.2", + "NeedsCompilation": "yes", + "Author": "Gábor Csárdi [aut, cre], Hadley Wickham [ctb], Kirill Müller [ctb], Salim Brüggemann [ctb] (<https://orcid.org/0000-0002-5329-5987>), Posit Software, PBC [cph, fnd]", + "Maintainer": "Gábor Csárdi <gabor@posit.co>", + "Repository": "CRAN" + }, + "cluster": { + "Package": "cluster", + "Version": "2.1.8", + "Source": "Repository", + "VersionNote": "Last CRAN: 2.1.7 on 2024-12-06; 2.1.6 on 2023-11-30; 2.1.5 on 2023-11-27", + "Date": "2024-12-10", + "Priority": "recommended", + "Title": "\"Finding Groups in Data\": Cluster Analysis Extended Rousseeuw et al.", + "Description": "Methods for Cluster analysis. Much extended the original from Peter Rousseeuw, Anja Struyf and Mia Hubert, based on Kaufman and Rousseeuw (1990) \"Finding Groups in Data\".", + "Maintainer": "Martin Maechler <maechler@stat.math.ethz.ch>", + "Authors@R": "c(person(\"Martin\",\"Maechler\", role = c(\"aut\",\"cre\"), email=\"maechler@stat.math.ethz.ch\", comment = c(ORCID = \"0000-0002-8685-9910\")) ,person(\"Peter\", \"Rousseeuw\", role=\"aut\", email=\"peter.rousseeuw@kuleuven.be\", comment = c(\"Fortran original\", ORCID = \"0000-0002-3807-5353\")) ,person(\"Anja\", \"Struyf\", role=\"aut\", comment= \"S original\") ,person(\"Mia\", \"Hubert\", role=\"aut\", email= \"Mia.Hubert@uia.ua.ac.be\", comment = c(\"S original\", ORCID = \"0000-0001-6398-4850\")) ,person(\"Kurt\", \"Hornik\", role=c(\"trl\", \"ctb\"), email=\"Kurt.Hornik@R-project.org\", comment=c(\"port to R; maintenance(1999-2000)\", ORCID=\"0000-0003-4198-9911\")) ,person(\"Matthias\", \"Studer\", role=\"ctb\") ,person(\"Pierre\", \"Roudier\", role=\"ctb\") ,person(\"Juan\", \"Gonzalez\", role=\"ctb\") ,person(\"Kamil\", \"Kozlowski\", role=\"ctb\") ,person(\"Erich\", \"Schubert\", role=\"ctb\", comment = c(\"fastpam options for pam()\", ORCID = \"0000-0001-9143-4880\")) ,person(\"Keefe\", \"Murphy\", role=\"ctb\", comment = \"volume.ellipsoid({d >= 3})\") #not yet ,person(\"Fischer-Rasmussen\", \"Kasper\", role = \"ctb\", comment = \"Gower distance for CLARA\") )", + "Depends": [ + "R (>= 3.5.0)" + ], + "Imports": [ + "graphics", + "grDevices", + "stats", + "utils" + ], + "Suggests": [ + "MASS", + "Matrix" + ], + "SuggestsNote": "MASS: two examples using cov.rob() and mvrnorm(); Matrix tools for testing", + "Enhances": [ + "mvoutlier", + "fpc", + "ellipse", + "sfsmisc" + ], + "EnhancesNote": "xref-ed in man/*.Rd", + "LazyLoad": "yes", + "LazyData": "yes", + "ByteCompile": "yes", + "BuildResaveData": "no", + "License": "GPL (>= 2)", + "URL": "https://svn.r-project.org/R-packages/trunk/cluster/", + "NeedsCompilation": "yes", + "Author": "Martin Maechler [aut, cre] (<https://orcid.org/0000-0002-8685-9910>), Peter Rousseeuw [aut] (Fortran original, <https://orcid.org/0000-0002-3807-5353>), Anja Struyf [aut] (S original), Mia Hubert [aut] (S original, <https://orcid.org/0000-0001-6398-4850>), Kurt Hornik [trl, ctb] (port to R; maintenance(1999-2000), <https://orcid.org/0000-0003-4198-9911>), Matthias Studer [ctb], Pierre Roudier [ctb], Juan Gonzalez [ctb], Kamil Kozlowski [ctb], Erich Schubert [ctb] (fastpam options for pam(), <https://orcid.org/0000-0001-9143-4880>), Keefe Murphy [ctb] (volume.ellipsoid({d >= 3}))", + "Repository": "CRAN" + }, + "colorspace": { + "Package": "colorspace", + "Version": "2.1-1", + "Source": "Repository", + "Date": "2024-07-26", + "Title": "A Toolbox for Manipulating and Assessing Colors and Palettes", + "Authors@R": "c(person(given = \"Ross\", family = \"Ihaka\", role = \"aut\", email = \"ihaka@stat.auckland.ac.nz\"), person(given = \"Paul\", family = \"Murrell\", role = \"aut\", email = \"paul@stat.auckland.ac.nz\", comment = c(ORCID = \"0000-0002-3224-8858\")), person(given = \"Kurt\", family = \"Hornik\", role = \"aut\", email = \"Kurt.Hornik@R-project.org\", comment = c(ORCID = \"0000-0003-4198-9911\")), person(given = c(\"Jason\", \"C.\"), family = \"Fisher\", role = \"aut\", email = \"jfisher@usgs.gov\", comment = c(ORCID = \"0000-0001-9032-8912\")), person(given = \"Reto\", family = \"Stauffer\", role = \"aut\", email = \"Reto.Stauffer@uibk.ac.at\", comment = c(ORCID = \"0000-0002-3798-5507\")), person(given = c(\"Claus\", \"O.\"), family = \"Wilke\", role = \"aut\", email = \"wilke@austin.utexas.edu\", comment = c(ORCID = \"0000-0002-7470-9261\")), person(given = c(\"Claire\", \"D.\"), family = \"McWhite\", role = \"aut\", email = \"claire.mcwhite@utmail.utexas.edu\", comment = c(ORCID = \"0000-0001-7346-3047\")), person(given = \"Achim\", family = \"Zeileis\", role = c(\"aut\", \"cre\"), email = \"Achim.Zeileis@R-project.org\", comment = c(ORCID = \"0000-0003-0918-3766\")))", + "Description": "Carries out mapping between assorted color spaces including RGB, HSV, HLS, CIEXYZ, CIELUV, HCL (polar CIELUV), CIELAB, and polar CIELAB. Qualitative, sequential, and diverging color palettes based on HCL colors are provided along with corresponding ggplot2 color scales. Color palette choice is aided by an interactive app (with either a Tcl/Tk or a shiny graphical user interface) and shiny apps with an HCL color picker and a color vision deficiency emulator. Plotting functions for displaying and assessing palettes include color swatches, visualizations of the HCL space, and trajectories in HCL and/or RGB spectrum. Color manipulation functions include: desaturation, lightening/darkening, mixing, and simulation of color vision deficiencies (deutanomaly, protanomaly, tritanomaly). Details can be found on the project web page at <https://colorspace.R-Forge.R-project.org/> and in the accompanying scientific paper: Zeileis et al. (2020, Journal of Statistical Software, <doi:10.18637/jss.v096.i01>).", + "Depends": [ + "R (>= 3.0.0)", + "methods" + ], + "Imports": [ + "graphics", + "grDevices", + "stats" + ], + "Suggests": [ + "datasets", + "utils", + "KernSmooth", + "MASS", + "kernlab", + "mvtnorm", + "vcd", + "tcltk", + "shiny", + "shinyjs", + "ggplot2", + "dplyr", + "scales", + "grid", + "png", + "jpeg", + "knitr", + "rmarkdown", + "RColorBrewer", + "rcartocolor", + "scico", + "viridis", + "wesanderson" + ], + "VignetteBuilder": "knitr", + "License": "BSD_3_clause + file LICENSE", + "URL": "https://colorspace.R-Forge.R-project.org/, https://hclwizard.org/", + "BugReports": "https://colorspace.R-Forge.R-project.org/contact.html", + "LazyData": "yes", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.1", + "NeedsCompilation": "yes", + "Author": "Ross Ihaka [aut], Paul Murrell [aut] (<https://orcid.org/0000-0002-3224-8858>), Kurt Hornik [aut] (<https://orcid.org/0000-0003-4198-9911>), Jason C. Fisher [aut] (<https://orcid.org/0000-0001-9032-8912>), Reto Stauffer [aut] (<https://orcid.org/0000-0002-3798-5507>), Claus O. Wilke [aut] (<https://orcid.org/0000-0002-7470-9261>), Claire D. McWhite [aut] (<https://orcid.org/0000-0001-7346-3047>), Achim Zeileis [aut, cre] (<https://orcid.org/0000-0003-0918-3766>)", + "Maintainer": "Achim Zeileis <Achim.Zeileis@R-project.org>", + "Repository": "CRAN" + }, + "commonmark": { + "Package": "commonmark", + "Version": "1.9.2", + "Source": "Repository", + "Type": "Package", + "Title": "High Performance CommonMark and Github Markdown Rendering in R", + "Authors@R": "c( person(\"Jeroen\", \"Ooms\", ,\"jeroenooms@gmail.com\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-4035-0289\")), person(\"John MacFarlane\", role = \"cph\", comment = \"Author of cmark\"))", + "Description": "The CommonMark specification <https://github.github.com/gfm/> defines a rationalized version of markdown syntax. This package uses the 'cmark' reference implementation for converting markdown text into various formats including html, latex and groff man. In addition it exposes the markdown parse tree in xml format. Also includes opt-in support for GFM extensions including tables, autolinks, and strikethrough text.", + "License": "BSD_2_clause + file LICENSE", + "URL": "https://docs.ropensci.org/commonmark/ https://ropensci.r-universe.dev/commonmark", + "BugReports": "https://github.com/r-lib/commonmark/issues", + "Suggests": [ + "curl", + "testthat", + "xml2" + ], + "RoxygenNote": "7.2.3", + "Language": "en-US", + "Encoding": "UTF-8", + "NeedsCompilation": "yes", + "Author": "Jeroen Ooms [aut, cre] (<https://orcid.org/0000-0002-4035-0289>), John MacFarlane [cph] (Author of cmark)", + "Maintainer": "Jeroen Ooms <jeroenooms@gmail.com>", + "Repository": "CRAN" + }, + "config": { + "Package": "config", + "Version": "0.3.2", + "Source": "Repository", + "Type": "Package", + "Title": "Manage Environment Specific Configuration Values", + "Authors@R": "c( person(\"JJ\", \"Allaire\", role = c(\"aut\"), email = \"jj@rstudio.com\"), person(\"Andrie\", \"de Vries\", role = \"cre\", email = \"apdevries@gmail.com\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", + "Imports": [ + "yaml (>= 2.1.19)" + ], + "Suggests": [ + "testthat", + "knitr", + "rmarkdown", + "covr", + "spelling", + "withr" + ], + "Description": "Manage configuration values across multiple environments (e.g. development, test, production). Read values using a function that determines the current environment and returns the appropriate value.", + "License": "GPL-3", + "URL": "https://rstudio.github.io/config/, https://github.com/rstudio/config", + "BugReports": "https://github.com/rstudio/config/issues", + "RoxygenNote": "7.2.3", + "VignetteBuilder": "knitr", + "Encoding": "UTF-8", + "Language": "en-US", + "Config/testthat/edition": "3", + "NeedsCompilation": "no", + "Author": "JJ Allaire [aut], Andrie de Vries [cre], Posit Software, PBC [cph, fnd]", + "Maintainer": "Andrie de Vries <apdevries@gmail.com>", + "Repository": "CRAN" + }, + "cpp11": { + "Package": "cpp11", + "Version": "0.5.1", + "Source": "Repository", + "Title": "A C++11 Interface for R's C Interface", + "Authors@R": "c( person(\"Davis\", \"Vaughan\", email = \"davis@posit.co\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0003-4777-038X\")), person(\"Jim\",\"Hester\", role = \"aut\", comment = c(ORCID = \"0000-0002-2739-7082\")), person(\"Romain\", \"François\", role = \"aut\", comment = c(ORCID = \"0000-0002-2444-4226\")), person(\"Benjamin\", \"Kietzman\", role = \"ctb\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", + "Description": "Provides a header only, C++11 interface to R's C interface. Compared to other approaches 'cpp11' strives to be safe against long jumps from the C API as well as C++ exceptions, conform to normal R function semantics and supports interaction with 'ALTREP' vectors.", + "License": "MIT + file LICENSE", + "URL": "https://cpp11.r-lib.org, https://github.com/r-lib/cpp11", + "BugReports": "https://github.com/r-lib/cpp11/issues", + "Depends": [ + "R (>= 4.0.0)" + ], + "Suggests": [ + "bench", + "brio", + "callr", + "cli", + "covr", + "decor", + "desc", + "ggplot2", + "glue", + "knitr", + "lobstr", + "mockery", + "progress", + "rmarkdown", + "scales", + "Rcpp", + "testthat (>= 3.2.0)", + "tibble", + "utils", + "vctrs", + "withr" + ], + "VignetteBuilder": "knitr", + "Config/Needs/website": "tidyverse/tidytemplate", + "Config/testthat/edition": "3", + "Config/Needs/cpp11/cpp_register": "brio, cli, decor, desc, glue, tibble, vctrs", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.2", + "NeedsCompilation": "no", + "Author": "Davis Vaughan [aut, cre] (<https://orcid.org/0000-0003-4777-038X>), Jim Hester [aut] (<https://orcid.org/0000-0002-2739-7082>), Romain François [aut] (<https://orcid.org/0000-0002-2444-4226>), Benjamin Kietzman [ctb], Posit Software, PBC [cph, fnd]", + "Maintainer": "Davis Vaughan <davis@posit.co>", + "Repository": "CRAN" + }, + "crayon": { + "Package": "crayon", + "Version": "1.5.3", + "Source": "Repository", + "Title": "Colored Terminal Output", + "Authors@R": "c( person(\"Gábor\", \"Csárdi\", , \"csardi.gabor@gmail.com\", role = c(\"aut\", \"cre\")), person(\"Brodie\", \"Gaslam\", , \"brodie.gaslam@yahoo.com\", role = \"ctb\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", + "Description": "The crayon package is now superseded. Please use the 'cli' package for new projects. Colored terminal output on terminals that support 'ANSI' color and highlight codes. It also works in 'Emacs' 'ESS'. 'ANSI' color support is automatically detected. Colors and highlighting can be combined and nested. New styles can also be created easily. This package was inspired by the 'chalk' 'JavaScript' project.", + "License": "MIT + file LICENSE", + "URL": "https://r-lib.github.io/crayon/, https://github.com/r-lib/crayon", + "BugReports": "https://github.com/r-lib/crayon/issues", + "Imports": [ + "grDevices", + "methods", + "utils" + ], + "Suggests": [ + "mockery", + "rstudioapi", + "testthat", + "withr" + ], + "Config/Needs/website": "tidyverse/tidytemplate", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.1", + "Collate": "'aaa-rstudio-detect.R' 'aaaa-rematch2.R' 'aab-num-ansi-colors.R' 'aac-num-ansi-colors.R' 'ansi-256.R' 'ansi-palette.R' 'combine.R' 'string.R' 'utils.R' 'crayon-package.R' 'disposable.R' 'enc-utils.R' 'has_ansi.R' 'has_color.R' 'link.R' 'styles.R' 'machinery.R' 'parts.R' 'print.R' 'style-var.R' 'show.R' 'string_operations.R'", + "NeedsCompilation": "no", + "Author": "Gábor Csárdi [aut, cre], Brodie Gaslam [ctb], Posit Software, PBC [cph, fnd]", + "Maintainer": "Gábor Csárdi <csardi.gabor@gmail.com>", + "Repository": "CRAN" + }, + "crosstalk": { + "Package": "crosstalk", + "Version": "1.2.1", + "Source": "Repository", + "Type": "Package", + "Title": "Inter-Widget Interactivity for HTML Widgets", + "Authors@R": "c( person(\"Joe\", \"Cheng\", role = \"aut\", email = \"joe@posit.co\"), person(\"Carson\", \"Sievert\", role = c(\"aut\", \"cre\"), email = \"carson@posit.co\", comment = c(ORCID = \"0000-0002-4958-2844\")), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")), person(family = \"jQuery Foundation\", role = \"cph\", comment = \"jQuery library and jQuery UI library\"), person(family = \"jQuery contributors\", role = c(\"ctb\", \"cph\"), comment = \"jQuery library; authors listed in inst/www/shared/jquery-AUTHORS.txt\"), person(\"Mark\", \"Otto\", role = \"ctb\", comment = \"Bootstrap library\"), person(\"Jacob\", \"Thornton\", role = \"ctb\", comment = \"Bootstrap library\"), person(family = \"Bootstrap contributors\", role = \"ctb\", comment = \"Bootstrap library\"), person(family = \"Twitter, Inc\", role = \"cph\", comment = \"Bootstrap library\"), person(\"Brian\", \"Reavis\", role = c(\"ctb\", \"cph\"), comment = \"selectize.js library\"), person(\"Kristopher Michael\", \"Kowal\", role = c(\"ctb\", \"cph\"), comment = \"es5-shim library\"), person(family = \"es5-shim contributors\", role = c(\"ctb\", \"cph\"), comment = \"es5-shim library\"), person(\"Denis\", \"Ineshin\", role = c(\"ctb\", \"cph\"), comment = \"ion.rangeSlider library\"), person(\"Sami\", \"Samhuri\", role = c(\"ctb\", \"cph\"), comment = \"Javascript strftime library\") )", + "Description": "Provides building blocks for allowing HTML widgets to communicate with each other, with Shiny or without (i.e. static .html files). Currently supports linked brushing and filtering.", + "License": "MIT + file LICENSE", + "Imports": [ + "htmltools (>= 0.3.6)", + "jsonlite", + "lazyeval", + "R6" + ], + "Suggests": [ + "shiny", + "ggplot2", + "testthat (>= 2.1.0)", + "sass", + "bslib" + ], + "URL": "https://rstudio.github.io/crosstalk/, https://github.com/rstudio/crosstalk", + "BugReports": "https://github.com/rstudio/crosstalk/issues", + "RoxygenNote": "7.2.3", + "Encoding": "UTF-8", + "NeedsCompilation": "no", + "Author": "Joe Cheng [aut], Carson Sievert [aut, cre] (<https://orcid.org/0000-0002-4958-2844>), Posit Software, PBC [cph, fnd], jQuery Foundation [cph] (jQuery library and jQuery UI library), jQuery contributors [ctb, cph] (jQuery library; authors listed in inst/www/shared/jquery-AUTHORS.txt), Mark Otto [ctb] (Bootstrap library), Jacob Thornton [ctb] (Bootstrap library), Bootstrap contributors [ctb] (Bootstrap library), Twitter, Inc [cph] (Bootstrap library), Brian Reavis [ctb, cph] (selectize.js library), Kristopher Michael Kowal [ctb, cph] (es5-shim library), es5-shim contributors [ctb, cph] (es5-shim library), Denis Ineshin [ctb, cph] (ion.rangeSlider library), Sami Samhuri [ctb, cph] (Javascript strftime library)", + "Maintainer": "Carson Sievert <carson@posit.co>", + "Repository": "CRAN" + }, + "curl": { + "Package": "curl", + "Version": "6.2.1", + "Source": "Repository", + "Type": "Package", + "Title": "A Modern and Flexible Web Client for R", + "Authors@R": "c( person(\"Jeroen\", \"Ooms\", role = c(\"aut\", \"cre\"), email = \"jeroenooms@gmail.com\", comment = c(ORCID = \"0000-0002-4035-0289\")), person(\"Hadley\", \"Wickham\", role = \"ctb\"), person(\"Posit Software, PBC\", role = \"cph\"))", + "Description": "Bindings to 'libcurl' <https://curl.se/libcurl/> for performing fully configurable HTTP/FTP requests where responses can be processed in memory, on disk, or streaming via the callback or connection interfaces. 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Gorecki [aut], Michael Chirico [aut] (<https://orcid.org/0000-0003-0787-087X>), Toby Hocking [aut] (<https://orcid.org/0000-0002-3146-0865>), Benjamin Schwendinger [aut] (<https://orcid.org/0000-0003-3315-8114>), Ivan Krylov [aut] (<https://orcid.org/0000-0002-0172-3812>), Pasha Stetsenko [ctb], Tom Short [ctb], Steve Lianoglou [ctb], Eduard Antonyan [ctb], Markus Bonsch [ctb], Hugh Parsonage [ctb], Scott Ritchie [ctb], Kun Ren [ctb], Xianying Tan [ctb], Rick Saporta [ctb], Otto Seiskari [ctb], Xianghui Dong [ctb], Michel Lang [ctb], Watal Iwasaki [ctb], Seth Wenchel [ctb], Karl Broman [ctb], Tobias Schmidt [ctb], David Arenburg [ctb], Ethan Smith [ctb], Francois Cocquemas [ctb], Matthieu Gomez [ctb], Philippe Chataignon [ctb], Nello Blaser [ctb], Dmitry Selivanov [ctb], Andrey Riabushenko [ctb], Cheng Lee [ctb], Declan Groves [ctb], Daniel Possenriede [ctb], Felipe Parages [ctb], Denes Toth [ctb], Mus Yaramaz-David [ctb], Ayappan Perumal [ctb], James Sams [ctb], Martin Morgan [ctb], 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Sluga [ctb], Bill Evans [ctb]", + "Maintainer": "Tyson Barrett <t.barrett88@gmail.com>", + "Repository": "CRAN" + }, + "desc": { + "Package": "desc", + "Version": "1.4.3", + "Source": "Repository", + "Title": "Manipulate DESCRIPTION Files", + "Authors@R": "c( person(\"Gábor\", \"Csárdi\", , \"csardi.gabor@gmail.com\", role = c(\"aut\", \"cre\")), person(\"Kirill\", \"Müller\", role = \"aut\"), person(\"Jim\", \"Hester\", , \"james.f.hester@gmail.com\", role = \"aut\"), person(\"Maëlle\", \"Salmon\", role = \"ctb\", comment = c(ORCID = \"0000-0002-2815-0399\")), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", + "Maintainer": "Gábor Csárdi <csardi.gabor@gmail.com>", + "Description": "Tools to read, write, create, and manipulate DESCRIPTION files. It is intended for packages that create or manipulate other packages.", + "License": "MIT + file LICENSE", + "URL": "https://desc.r-lib.org/, https://github.com/r-lib/desc", + "BugReports": "https://github.com/r-lib/desc/issues", + "Depends": [ + "R (>= 3.4)" + ], + "Imports": [ + "cli", + "R6", + "utils" + ], + "Suggests": [ + "callr", + "covr", + "gh", + "spelling", + "testthat", + "whoami", + "withr" + ], + "Config/Needs/website": "tidyverse/tidytemplate", + "Config/testthat/edition": "3", + "Encoding": "UTF-8", + "Language": "en-US", + "RoxygenNote": "7.2.3", + "Collate": "'assertions.R' 'authors-at-r.R' 'built.R' 'classes.R' 'collate.R' 'constants.R' 'deps.R' 'desc-package.R' 'description.R' 'encoding.R' 'find-package-root.R' 'latex.R' 'non-oo-api.R' 'package-archives.R' 'read.R' 'remotes.R' 'str.R' 'syntax_checks.R' 'urls.R' 'utils.R' 'validate.R' 'version.R'", + "NeedsCompilation": "no", + "Author": "Gábor Csárdi [aut, cre], Kirill Müller [aut], Jim Hester [aut], Maëlle Salmon [ctb] (<https://orcid.org/0000-0002-2815-0399>), Posit Software, PBC [cph, fnd]", + "Repository": "CRAN" + }, + "digest": { + "Package": "digest", + "Version": "0.6.37", + "Source": "Repository", + "Authors@R": "c(person(\"Dirk\", \"Eddelbuettel\", role = c(\"aut\", \"cre\"), email = \"edd@debian.org\", comment = c(ORCID = \"0000-0001-6419-907X\")), person(\"Antoine\", \"Lucas\", role=\"ctb\"), person(\"Jarek\", \"Tuszynski\", role=\"ctb\"), person(\"Henrik\", \"Bengtsson\", role=\"ctb\", comment = c(ORCID = \"0000-0002-7579-5165\")), person(\"Simon\", \"Urbanek\", role=\"ctb\", comment = c(ORCID = \"0000-0003-2297-1732\")), person(\"Mario\", \"Frasca\", role=\"ctb\"), person(\"Bryan\", \"Lewis\", role=\"ctb\"), person(\"Murray\", \"Stokely\", role=\"ctb\"), person(\"Hannes\", \"Muehleisen\", role=\"ctb\"), person(\"Duncan\", \"Murdoch\", role=\"ctb\"), person(\"Jim\", \"Hester\", role=\"ctb\"), person(\"Wush\", \"Wu\", role=\"ctb\", comment = c(ORCID = \"0000-0001-5180-0567\")), person(\"Qiang\", \"Kou\", role=\"ctb\", comment = c(ORCID = \"0000-0001-6786-5453\")), person(\"Thierry\", \"Onkelinx\", role=\"ctb\", comment = c(ORCID = \"0000-0001-8804-4216\")), person(\"Michel\", \"Lang\", role=\"ctb\", comment = c(ORCID = \"0000-0001-9754-0393\")), person(\"Viliam\", \"Simko\", role=\"ctb\"), person(\"Kurt\", \"Hornik\", role=\"ctb\", comment = c(ORCID = \"0000-0003-4198-9911\")), person(\"Radford\", \"Neal\", role=\"ctb\", comment = c(ORCID = \"0000-0002-2473-3407\")), person(\"Kendon\", \"Bell\", role=\"ctb\", comment = c(ORCID = \"0000-0002-9093-8312\")), person(\"Matthew\", \"de Queljoe\", role=\"ctb\"), person(\"Dmitry\", \"Selivanov\", role=\"ctb\"), person(\"Ion\", \"Suruceanu\", role=\"ctb\"), person(\"Bill\", \"Denney\", role=\"ctb\"), person(\"Dirk\", \"Schumacher\", role=\"ctb\"), person(\"András\", \"Svraka\", role=\"ctb\"), person(\"Sergey\", \"Fedorov\", role=\"ctb\"), person(\"Will\", \"Landau\", role=\"ctb\", comment = c(ORCID = \"0000-0003-1878-3253\")), person(\"Floris\", \"Vanderhaeghe\", role=\"ctb\", comment = c(ORCID = \"0000-0002-6378-6229\")), person(\"Kevin\", \"Tappe\", role=\"ctb\"), person(\"Harris\", \"McGehee\", role=\"ctb\"), person(\"Tim\", \"Mastny\", role=\"ctb\"), person(\"Aaron\", \"Peikert\", role=\"ctb\", comment = c(ORCID = \"0000-0001-7813-818X\")), person(\"Mark\", \"van der Loo\", role=\"ctb\", comment = c(ORCID = \"0000-0002-9807-4686\")), person(\"Chris\", \"Muir\", role=\"ctb\", comment = c(ORCID = \"0000-0003-2555-3878\")), person(\"Moritz\", \"Beller\", role=\"ctb\", comment = c(ORCID = \"0000-0003-4852-0526\")), person(\"Sebastian\", \"Campbell\", role=\"ctb\"), person(\"Winston\", \"Chang\", role=\"ctb\", comment = c(ORCID = \"0000-0002-1576-2126\")), person(\"Dean\", \"Attali\", role=\"ctb\", comment = c(ORCID = \"0000-0002-5645-3493\")), person(\"Michael\", \"Chirico\", role=\"ctb\", comment = c(ORCID = \"0000-0003-0787-087X\")), person(\"Kevin\", \"Ushey\", role=\"ctb\"))", + "Date": "2024-08-19", + "Title": "Create Compact Hash Digests of R Objects", + "Description": "Implementation of a function 'digest()' for the creation of hash digests of arbitrary R objects (using the 'md5', 'sha-1', 'sha-256', 'crc32', 'xxhash', 'murmurhash', 'spookyhash', 'blake3', 'crc32c', 'xxh3_64', and 'xxh3_128' algorithms) permitting easy comparison of R language objects, as well as functions such as'hmac()' to create hash-based message authentication code. Please note that this package is not meant to be deployed for cryptographic purposes for which more comprehensive (and widely tested) libraries such as 'OpenSSL' should be used.", + "URL": "https://github.com/eddelbuettel/digest, https://dirk.eddelbuettel.com/code/digest.html", + "BugReports": "https://github.com/eddelbuettel/digest/issues", + "Depends": [ + "R (>= 3.3.0)" + ], + "Imports": [ + "utils" + ], + "License": "GPL (>= 2)", + "Suggests": [ + "tinytest", + "simplermarkdown" + ], + "VignetteBuilder": "simplermarkdown", + "Encoding": "UTF-8", + "NeedsCompilation": "yes", + "Author": "Dirk Eddelbuettel [aut, cre] (<https://orcid.org/0000-0001-6419-907X>), Antoine Lucas [ctb], Jarek Tuszynski [ctb], Henrik Bengtsson [ctb] (<https://orcid.org/0000-0002-7579-5165>), Simon Urbanek [ctb] (<https://orcid.org/0000-0003-2297-1732>), Mario Frasca [ctb], Bryan Lewis [ctb], Murray Stokely [ctb], Hannes Muehleisen [ctb], Duncan Murdoch [ctb], Jim Hester [ctb], Wush Wu [ctb] 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Source code of other languages is supported via Andre Simon's highlight package (<https://gitlab.com/saalen/highlight>).", + "Depends": [ + "R (>= 3.3.0)" + ], + "Imports": [ + "xfun (>= 0.18)" + ], + "Suggests": [ + "knitr", + "markdown", + "testit" + ], + "License": "GPL", + "URL": "https://github.com/yihui/highr", + "BugReports": "https://github.com/yihui/highr/issues", + "VignetteBuilder": "knitr", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.1", + "NeedsCompilation": "no", + "Author": "Yihui Xie [aut, cre] (<https://orcid.org/0000-0003-0645-5666>), Yixuan Qiu [aut], Christopher Gandrud [ctb], Qiang Li [ctb]", + "Maintainer": "Yihui Xie <xie@yihui.name>", + "Repository": "CRAN" + }, + "hms": { + "Package": "hms", + "Version": "1.1.3", + "Source": "Repository", + "Title": "Pretty Time of Day", + "Date": "2023-03-21", + "Authors@R": "c( person(\"Kirill\", \"Müller\", role = c(\"aut\", \"cre\"), email = \"kirill@cynkra.com\", comment = c(ORCID = \"0000-0002-1416-3412\")), person(\"R Consortium\", role = \"fnd\"), person(\"RStudio\", role = \"fnd\") )", + "Description": "Implements an S3 class for storing and formatting time-of-day values, based on the 'difftime' class.", + "Imports": [ + "lifecycle", + "methods", + "pkgconfig", + "rlang (>= 1.0.2)", + "vctrs (>= 0.3.8)" + ], + "Suggests": [ + "crayon", + "lubridate", + "pillar (>= 1.1.0)", + "testthat (>= 3.0.0)" + ], + "License": "MIT + file LICENSE", + "Encoding": "UTF-8", + "URL": "https://hms.tidyverse.org/, https://github.com/tidyverse/hms", + "BugReports": "https://github.com/tidyverse/hms/issues", + "RoxygenNote": "7.2.3", + "Config/testthat/edition": "3", + "Config/autostyle/scope": "line_breaks", + "Config/autostyle/strict": "false", + "Config/Needs/website": "tidyverse/tidytemplate", + "NeedsCompilation": "no", + "Author": "Kirill Müller [aut, cre] (<https://orcid.org/0000-0002-1416-3412>), R Consortium [fnd], RStudio [fnd]", + "Maintainer": "Kirill Müller <kirill@cynkra.com>", + "Repository": "CRAN" + }, + "htmlTable": { + "Package": "htmlTable", + "Version": "2.4.3", + "Source": "Repository", + "Title": "Advanced Tables for Markdown/HTML", + "Authors@R": "c( person(\"Max\", \"Gordon\", email = \"max@gforge.se\", role = c(\"aut\", \"cre\")), person(\"Stephen\", \"Gragg\", role=c(\"aut\")), person(\"Peter\", \"Konings\", role=c(\"aut\")))", + "Maintainer": "Max Gordon <max@gforge.se>", + "Description": "Tables with state-of-the-art layout elements such as row spanners, column spanners, table spanners, zebra striping, and more. While allowing advanced layout, the underlying css-structure is simple in order to maximize compatibility with common word processors. 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\"ctb\"), person(\"Jeroen\", \"Ooms\", role = \"ctb\"), person(\"Andrzej\", \"Krzemienski\", role = \"cph\", comment = \"optional.hpp\"), person(\"libuv project contributors\", role = \"cph\", comment = \"libuv library, see src/libuv/AUTHORS file\"), person(\"Joyent, Inc. and other Node contributors\", role = \"cph\", comment = \"libuv library, see src/libuv/AUTHORS file; and http-parser library, see src/http-parser/AUTHORS file\"), person(\"Niels\", \"Provos\", role = \"cph\", comment = \"libuv subcomponent: tree.h\"), person(\"Internet Systems Consortium, Inc.\", role = \"cph\", comment = \"libuv subcomponent: inet_pton and inet_ntop, contained in src/libuv/src/inet.c\"), person(\"Alexander\", \"Chemeris\", role = \"cph\", comment = \"libuv subcomponent: stdint-msvc2008.h (from msinttypes)\"), person(\"Google, Inc.\", role = \"cph\", comment = \"libuv subcomponent: pthread-fixes.c\"), person(\"Sony Mobile Communcations AB\", role = \"cph\", comment = \"libuv subcomponent: 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for handling HTTP and WebSocket requests directly from within R. It is primarily intended as a building block for other packages, rather than making it particularly easy to create complete web applications using httpuv alone. httpuv is built on top of the libuv and http-parser C libraries, both of which were developed by Joyent, Inc. (See LICENSE file for libuv and http-parser license information.)", + "License": "GPL (>= 2) | file LICENSE", + "URL": "https://github.com/rstudio/httpuv", + "BugReports": "https://github.com/rstudio/httpuv/issues", + "Depends": [ + "R (>= 2.15.1)" + ], + "Imports": [ + "later (>= 0.8.0)", + "promises", + "R6", + "Rcpp (>= 1.0.7)", + "utils" + ], + "Suggests": [ + "callr", + "curl", + "testthat", + "websocket" + ], + "LinkingTo": [ + "later", + "Rcpp" + ], + "Encoding": "UTF-8", + "RoxygenNote": "7.3.1", + "SystemRequirements": "GNU make, zlib", + "Collate": "'RcppExports.R' 'httpuv.R' 'random_port.R' 'server.R' 'staticServer.R' 'static_paths.R' 'utils.R'", + "NeedsCompilation": "yes", + "Author": "Joe Cheng [aut], Winston Chang [aut, cre], Posit, PBC fnd [cph], Hector Corrada Bravo [ctb], Jeroen Ooms [ctb], Andrzej Krzemienski [cph] (optional.hpp), libuv project contributors [cph] (libuv library, see src/libuv/AUTHORS file), Joyent, Inc. and other Node contributors [cph] (libuv library, see src/libuv/AUTHORS file; and http-parser library, see src/http-parser/AUTHORS file), Niels Provos [cph] (libuv subcomponent: tree.h), Internet Systems Consortium, Inc. [cph] (libuv subcomponent: inet_pton and inet_ntop, contained in src/libuv/src/inet.c), Alexander Chemeris [cph] (libuv subcomponent: stdint-msvc2008.h (from msinttypes)), Google, Inc. [cph] (libuv subcomponent: pthread-fixes.c), Sony Mobile Communcations AB [cph] (libuv subcomponent: pthread-fixes.c), Berkeley Software Design Inc. [cph] (libuv subcomponent: android-ifaddrs.h, android-ifaddrs.c), Kenneth MacKay [cph] (libuv subcomponent: android-ifaddrs.h, android-ifaddrs.c), Emergya (Cloud4all, FP7/2007-2013, grant agreement no 289016) [cph] (libuv subcomponent: android-ifaddrs.h, android-ifaddrs.c), Steve Reid [aut] (SHA-1 implementation), James Brown [aut] (SHA-1 implementation), Bob Trower [aut] (base64 implementation), Alexander Peslyak [aut] (MD5 implementation), Trantor Standard Systems [cph] (base64 implementation), Igor Sysoev [cph] (http-parser)", + "Maintainer": "Winston Chang <winston@posit.co>", + "Repository": "CRAN" + }, + "httr": { + "Package": "httr", + "Version": "1.4.7", + "Source": "Repository", + "Title": "Tools for Working with URLs and HTTP", + "Authors@R": "c( person(\"Hadley\", \"Wickham\", , \"hadley@posit.co\", role = c(\"aut\", \"cre\")), person(\"Posit, PBC\", role = c(\"cph\", \"fnd\")) )", + "Description": "Useful tools for working with HTTP organised by HTTP verbs (GET(), POST(), etc). Configuration functions make it easy to control additional request components (authenticate(), add_headers() and so on).", + "License": "MIT + file LICENSE", + "URL": "https://httr.r-lib.org/, https://github.com/r-lib/httr", + "BugReports": "https://github.com/r-lib/httr/issues", + "Depends": [ + "R (>= 3.5)" + ], + "Imports": [ + "curl (>= 5.0.2)", + "jsonlite", + "mime", + "openssl (>= 0.8)", + "R6" + ], + "Suggests": [ + "covr", + "httpuv", + "jpeg", + "knitr", + "png", + "readr", + "rmarkdown", + "testthat (>= 0.8.0)", + "xml2" + ], + "VignetteBuilder": "knitr", + "Config/Needs/website": "tidyverse/tidytemplate", + "Encoding": "UTF-8", + "RoxygenNote": "7.2.3", + "NeedsCompilation": "no", + "Author": "Hadley Wickham [aut, cre], Posit, PBC [cph, fnd]", + "Maintainer": "Hadley Wickham <hadley@posit.co>", + "Repository": "CRAN" + }, + "intervals": { + "Package": "intervals", + "Version": "0.15.5", + "Source": "Repository", + "Type": "Package", + "Title": "Tools for Working with Points and Intervals", + "Authors@R": "c(person(given = \"Richard\", family = \"Bourgon\", role = \"aut\", email = \"bourgon.richard@gene.com\"), person(given = \"Edzer\", family = \"Pebesma\", role = \"cre\", email = \"edzer.pebesma@uni-muenster.de\"))", + "Depends": [ + "R (>= 2.9.0)" + ], + "Imports": [ + "utils", + "graphics", + "methods" + ], + "Description": "Tools for working with and comparing sets of points and intervals.", + "License": "Artistic-2.0", + "LazyLoad": "yes", + "URL": "https://github.com/edzer/intervals", + "NeedsCompilation": "yes", + "Author": "Richard Bourgon [aut], Edzer Pebesma [cre]", + "Maintainer": "Edzer Pebesma <edzer.pebesma@uni-muenster.de>", + "Repository": "CRAN" + }, + "isoband": { + "Package": "isoband", + "Version": "0.2.7", + "Source": "Repository", + "Title": "Generate Isolines and Isobands from Regularly Spaced Elevation Grids", + "Authors@R": "c( person(\"Hadley\", \"Wickham\", , \"hadley@posit.co\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0003-4757-117X\")), person(\"Claus O.\", \"Wilke\", , \"wilke@austin.utexas.edu\", role = \"aut\", comment = c(\"Original author\", ORCID = \"0000-0002-7470-9261\")), person(\"Thomas Lin\", \"Pedersen\", , \"thomasp85@gmail.com\", role = \"aut\", comment = c(ORCID = \"0000-0002-5147-4711\")) )", + "Description": "A fast C++ implementation to generate contour lines (isolines) and contour polygons (isobands) from regularly spaced grids containing elevation data.", + "License": "MIT + file LICENSE", + "URL": "https://isoband.r-lib.org", + "BugReports": "https://github.com/r-lib/isoband/issues", + "Imports": [ + "grid", + "utils" + ], + "Suggests": [ + "covr", + "ggplot2", + "knitr", + "magick", + "microbenchmark", + "rmarkdown", + "sf", + "testthat", + "xml2" + ], + "VignetteBuilder": "knitr", + "Config/Needs/website": "tidyverse/tidytemplate", + "Config/testthat/edition": "3", + "Encoding": "UTF-8", + "RoxygenNote": "7.2.3", + "SystemRequirements": "C++11", + "NeedsCompilation": "yes", + "Author": "Hadley Wickham [aut, cre] (<https://orcid.org/0000-0003-4757-117X>), Claus O. Wilke [aut] (Original author, <https://orcid.org/0000-0002-7470-9261>), Thomas Lin Pedersen [aut] (<https://orcid.org/0000-0002-5147-4711>)", + "Maintainer": "Hadley Wickham <hadley@posit.co>", + "Repository": "CRAN" + }, + "jquerylib": { + "Package": "jquerylib", + "Version": "0.1.4", + "Source": "Repository", + "Title": "Obtain 'jQuery' as an HTML Dependency Object", + "Authors@R": "c( person(\"Carson\", \"Sievert\", role = c(\"aut\", \"cre\"), email = \"carson@rstudio.com\", comment = c(ORCID = \"0000-0002-4958-2844\")), person(\"Joe\", \"Cheng\", role = \"aut\", email = \"joe@rstudio.com\"), person(family = \"RStudio\", role = \"cph\"), person(family = \"jQuery Foundation\", role = \"cph\", comment = \"jQuery library and jQuery UI library\"), person(family = \"jQuery contributors\", role = c(\"ctb\", \"cph\"), comment = \"jQuery library; authors listed in inst/lib/jquery-AUTHORS.txt\") )", + "Description": "Obtain any major version of 'jQuery' (<https://code.jquery.com/>) and use it in any webpage generated by 'htmltools' (e.g. 'shiny', 'htmlwidgets', and 'rmarkdown'). Most R users don't need to use this package directly, but other R packages (e.g. 'shiny', 'rmarkdown', etc.) depend on this package to avoid bundling redundant copies of 'jQuery'.", + "License": "MIT + file LICENSE", + "Encoding": "UTF-8", + "Config/testthat/edition": "3", + "RoxygenNote": "7.0.2", + "Imports": [ + "htmltools" + ], + "Suggests": [ + "testthat" + ], + "NeedsCompilation": "no", + "Author": "Carson Sievert [aut, cre] (<https://orcid.org/0000-0002-4958-2844>), Joe Cheng [aut], RStudio [cph], jQuery Foundation [cph] (jQuery library and jQuery UI library), jQuery contributors [ctb, cph] (jQuery library; authors listed in inst/lib/jquery-AUTHORS.txt)", + "Maintainer": "Carson Sievert <carson@rstudio.com>", + "Repository": "CRAN" + }, + "jsonlite": { + "Package": "jsonlite", + "Version": "1.9.0", + "Source": "Repository", + "Title": "A Simple and Robust JSON Parser and Generator for R", + "License": "MIT + file LICENSE", + "Depends": [ + "methods" + ], + "Authors@R": "c( person(\"Jeroen\", \"Ooms\", role = c(\"aut\", \"cre\"), email = \"jeroenooms@gmail.com\", comment = c(ORCID = \"0000-0002-4035-0289\")), person(\"Duncan\", \"Temple Lang\", role = \"ctb\"), person(\"Lloyd\", \"Hilaiel\", role = \"cph\", comment=\"author of bundled libyajl\"))", + "URL": "https://jeroen.r-universe.dev/jsonlite https://arxiv.org/abs/1403.2805", + "BugReports": "https://github.com/jeroen/jsonlite/issues", + "Maintainer": "Jeroen Ooms <jeroenooms@gmail.com>", + "VignetteBuilder": "knitr, R.rsp", + "Description": "A reasonably fast JSON parser and generator, optimized for statistical data and the web. Offers simple, flexible tools for working with JSON in R, and is particularly powerful for building pipelines and interacting with a web API. The implementation is based on the mapping described in the vignette (Ooms, 2014). In addition to converting JSON data from/to R objects, 'jsonlite' contains functions to stream, validate, and prettify JSON data. The unit tests included with the package verify that all edge cases are encoded and decoded consistently for use with dynamic data in systems and applications.", + "Suggests": [ + "httr", + "vctrs", + "testthat", + "knitr", + "rmarkdown", + "R.rsp", + "sf" + ], + "RoxygenNote": "7.2.3", + "Encoding": "UTF-8", + "NeedsCompilation": "yes", + "Author": "Jeroen Ooms [aut, cre] (<https://orcid.org/0000-0002-4035-0289>), Duncan Temple Lang [ctb], Lloyd Hilaiel [cph] (author of bundled libyajl)", + "Repository": "CRAN" + }, + "knitr": { + "Package": "knitr", + "Version": "1.49", + "Source": "Repository", + "Type": "Package", + "Title": "A General-Purpose Package for Dynamic Report Generation in R", + "Authors@R": "c( person(\"Yihui\", \"Xie\", role = c(\"aut\", \"cre\"), email = \"xie@yihui.name\", comment = c(ORCID = \"0000-0003-0645-5666\")), person(\"Abhraneel\", \"Sarma\", role = \"ctb\"), person(\"Adam\", \"Vogt\", role = \"ctb\"), person(\"Alastair\", \"Andrew\", role = \"ctb\"), 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The function rst2pdf() requires rst2pdf (https://github.com/rst2pdf/rst2pdf).", + "Collate": "'block.R' 'cache.R' 'utils.R' 'citation.R' 'hooks-html.R' 'plot.R' 'defaults.R' 'concordance.R' 'engine.R' 'highlight.R' 'themes.R' 'header.R' 'hooks-asciidoc.R' 'hooks-chunk.R' 'hooks-extra.R' 'hooks-latex.R' 'hooks-md.R' 'hooks-rst.R' 'hooks-textile.R' 'hooks.R' 'output.R' 'package.R' 'pandoc.R' 'params.R' 'parser.R' 'pattern.R' 'rocco.R' 'spin.R' 'table.R' 'template.R' 'utils-conversion.R' 'utils-rd2html.R' 'utils-string.R' 'utils-sweave.R' 'utils-upload.R' 'utils-vignettes.R' 'zzz.R'", + "RoxygenNote": "7.3.2", + "NeedsCompilation": "no", + "Author": "Yihui Xie [aut, cre] (<https://orcid.org/0000-0003-0645-5666>), Abhraneel Sarma [ctb], Adam Vogt [ctb], Alastair Andrew [ctb], Alex Zvoleff [ctb], Amar Al-Zubaidi [ctb], Andre Simon [ctb] (the CSS files under inst/themes/ were derived from the Highlight package http://www.andre-simon.de), Aron Atkins [ctb], Aaron Wolen [ctb], Ashley Manton [ctb], Atsushi Yasumoto [ctb] (<https://orcid.org/0000-0002-8335-495X>), Ben Baumer [ctb], Brian Diggs [ctb], Brian Zhang [ctb], Bulat Yapparov [ctb], Cassio Pereira [ctb], Christophe Dervieux [ctb], David Hall [ctb], David Hugh-Jones [ctb], David Robinson [ctb], Doug Hemken [ctb], Duncan Murdoch [ctb], Elio Campitelli [ctb], Ellis Hughes [ctb], Emily Riederer [ctb], Fabian Hirschmann [ctb], Fitch Simeon [ctb], Forest Fang [ctb], Frank E Harrell Jr [ctb] (the Sweavel package at inst/misc/Sweavel.sty), Garrick Aden-Buie [ctb], Gregoire Detrez [ctb], Hadley Wickham [ctb], Hao Zhu [ctb], Heewon Jeon [ctb], Henrik Bengtsson [ctb], Hiroaki Yutani [ctb], Ian Lyttle [ctb], Hodges Daniel [ctb], Jacob Bien [ctb], Jake Burkhead [ctb], James Manton [ctb], Jared Lander [ctb], Jason Punyon [ctb], Javier Luraschi [ctb], Jeff Arnold [ctb], Jenny Bryan [ctb], Jeremy Ashkenas [ctb, cph] (the CSS file at inst/misc/docco-classic.css), Jeremy Stephens [ctb], Jim Hester [ctb], Joe Cheng [ctb], Johannes Ranke [ctb], John Honaker [ctb], John Muschelli [ctb], Jonathan Keane [ctb], JJ Allaire [ctb], Johan Toloe [ctb], Jonathan Sidi [ctb], Joseph Larmarange [ctb], Julien Barnier [ctb], Kaiyin Zhong [ctb], Kamil Slowikowski [ctb], Karl Forner [ctb], Kevin K. 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Kamvar [ctb] (<https://orcid.org/0000-0003-1458-7108>), Posit Software, PBC [cph, fnd]", + "Maintainer": "Yihui Xie <xie@yihui.name>", + "Repository": "CRAN" + }, + "labeling": { + "Package": "labeling", + "Version": "0.4.3", + "Source": "Repository", + "Type": "Package", + "Title": "Axis Labeling", + "Date": "2023-08-29", + "Author": "Justin Talbot,", + "Maintainer": "Nuno Sempere <nuno.semperelh@gmail.com>", + "Description": "Functions which provide a range of axis labeling algorithms.", + "License": "MIT + file LICENSE | Unlimited", + "Collate": "'labeling.R'", + "NeedsCompilation": "no", + "Imports": [ + "stats", + "graphics" + ], + "Repository": "CRAN" + }, + "later": { + "Package": "later", + "Version": "1.4.1", + "Source": "Repository", + "Type": "Package", + "Title": "Utilities for Scheduling Functions to Execute Later with Event Loops", + "Authors@R": "c( person(\"Winston\", \"Chang\", role = c(\"aut\", \"cre\"), email = \"winston@posit.co\"), person(\"Joe\", \"Cheng\", role = c(\"aut\"), email = \"joe@posit.co\"), person(\"Charlie\", \"Gao\", role = c(\"aut\"), email = \"charlie.gao@shikokuchuo.net\", comment = c(ORCID = \"0000-0002-0750-061X\")), person(family = \"Posit Software, PBC\", role = \"cph\"), person(\"Marcus\", \"Geelnard\", role = c(\"ctb\", \"cph\"), comment = \"TinyCThread library, https://tinycthread.github.io/\"), person(\"Evan\", \"Nemerson\", role = c(\"ctb\", \"cph\"), comment = \"TinyCThread library, https://tinycthread.github.io/\") )", + "Description": "Executes arbitrary R or C functions some time after the current time, after the R execution stack has emptied. 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Provides a full implementation of LISP style 'quasiquotation', making it easier to generate code with other code.", + "Authors@R": "c( person(\"Hadley\", \"Wickham\", ,\"hadley@rstudio.com\", c(\"aut\", \"cre\")), person(\"RStudio\", role = \"cph\") )", + "License": "GPL-3", + "LazyData": "true", + "Depends": [ + "R (>= 3.1.0)" + ], + "Suggests": [ + "knitr", + "rmarkdown (>= 0.2.65)", + "testthat", + "covr" + ], + "VignetteBuilder": "knitr", + "RoxygenNote": "6.1.1", + "NeedsCompilation": "yes", + "Author": "Hadley Wickham [aut, cre], RStudio [cph]", + "Maintainer": "Hadley Wickham <hadley@rstudio.com>", + "Repository": "CRAN" + }, + "lifecycle": { + "Package": "lifecycle", + "Version": "1.0.4", + "Source": "Repository", + "Title": "Manage the Life Cycle of your Package Functions", + "Authors@R": "c( person(\"Lionel\", \"Henry\", , \"lionel@posit.co\", role = c(\"aut\", \"cre\")), person(\"Hadley\", \"Wickham\", , \"hadley@posit.co\", role = \"aut\", comment = c(ORCID = \"0000-0003-4757-117X\")), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", + "Description": "Manage the life cycle of your exported functions with shared conventions, documentation badges, and user-friendly deprecation warnings.", + "License": "MIT + file LICENSE", + "URL": "https://lifecycle.r-lib.org/, https://github.com/r-lib/lifecycle", + "BugReports": "https://github.com/r-lib/lifecycle/issues", + "Depends": [ + "R (>= 3.6)" + ], + "Imports": [ + "cli (>= 3.4.0)", + "glue", + "rlang (>= 1.1.0)" + ], + "Suggests": [ + "covr", + "crayon", + "knitr", + "lintr", + "rmarkdown", + "testthat (>= 3.0.1)", + "tibble", + "tidyverse", + "tools", + "vctrs", + "withr" + ], + "VignetteBuilder": "knitr", + "Config/Needs/website": "tidyverse/tidytemplate, usethis", + "Config/testthat/edition": "3", + "Encoding": "UTF-8", + "RoxygenNote": "7.2.1", + "NeedsCompilation": "no", + "Author": "Lionel Henry [aut, cre], Hadley Wickham [aut] (<https://orcid.org/0000-0003-4757-117X>), Posit Software, PBC [cph, fnd]", + "Maintainer": "Lionel Henry <lionel@posit.co>", + "Repository": "CRAN" + }, + "lubridate": { + "Package": "lubridate", + "Version": "1.9.4", + "Source": "Repository", + "Type": "Package", + "Title": "Make Dealing with Dates a Little Easier", + "Authors@R": "c( person(\"Vitalie\", \"Spinu\", , \"spinuvit@gmail.com\", role = c(\"aut\", \"cre\")), person(\"Garrett\", \"Grolemund\", role = \"aut\"), person(\"Hadley\", \"Wickham\", role = \"aut\"), person(\"Davis\", \"Vaughan\", role = \"ctb\"), person(\"Ian\", \"Lyttle\", role = \"ctb\"), person(\"Imanuel\", \"Costigan\", role = \"ctb\"), person(\"Jason\", \"Law\", role = \"ctb\"), person(\"Doug\", \"Mitarotonda\", role = \"ctb\"), person(\"Joseph\", \"Larmarange\", role = \"ctb\"), person(\"Jonathan\", \"Boiser\", role = \"ctb\"), person(\"Chel Hee\", \"Lee\", role = \"ctb\") )", + "Maintainer": "Vitalie Spinu <spinuvit@gmail.com>", + "Description": "Functions to work with date-times and time-spans: fast and user friendly parsing of date-time data, extraction and updating of components of a date-time (years, months, days, hours, minutes, and seconds), algebraic manipulation on date-time and time-span objects. The 'lubridate' package has a consistent and memorable syntax that makes working with dates easy and fun.", + "License": "GPL (>= 2)", + "URL": "https://lubridate.tidyverse.org, https://github.com/tidyverse/lubridate", + "BugReports": "https://github.com/tidyverse/lubridate/issues", + "Depends": [ + "methods", + "R (>= 3.2)" + ], + "Imports": [ + "generics", + "timechange (>= 0.3.0)" + ], + "Suggests": [ + "covr", + "knitr", + "rmarkdown", + "testthat (>= 2.1.0)", + "vctrs (>= 0.6.5)" + ], + "Enhances": [ + "chron", + "data.table", + "timeDate", + "tis", + "zoo" + ], + "VignetteBuilder": "knitr", + "Config/Needs/website": "tidyverse/tidytemplate", + "Config/testthat/edition": "3", + "Encoding": "UTF-8", + "LazyData": "true", + "RoxygenNote": "7.2.3", + "SystemRequirements": "C++11, A system with zoneinfo data (e.g. /usr/share/zoneinfo). 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library\"), person(\"John\", \"MacFarlane\", role = c(\"ctb\", \"cph\"), comment = \"Pandoc templates\"), person(, \"Google, Inc.\", role = c(\"ctb\", \"cph\"), comment = \"ioslides library\"), person(\"Dave\", \"Raggett\", role = \"ctb\", comment = \"slidy library\"), person(, \"W3C\", role = \"cph\", comment = \"slidy library\"), person(\"Dave\", \"Gandy\", role = c(\"ctb\", \"cph\"), comment = \"Font-Awesome\"), person(\"Ben\", \"Sperry\", role = \"ctb\", comment = \"Ionicons\"), person(, \"Drifty\", role = \"cph\", comment = \"Ionicons\"), person(\"Aidan\", \"Lister\", role = c(\"ctb\", \"cph\"), comment = \"jQuery StickyTabs\"), person(\"Benct Philip\", \"Jonsson\", role = c(\"ctb\", \"cph\"), comment = \"pagebreak Lua filter\"), person(\"Albert\", \"Krewinkel\", role = c(\"ctb\", \"cph\"), comment = \"pagebreak Lua filter\") )", + "Description": "Convert R Markdown documents into a variety of formats.", + "License": "GPL-3", + "URL": "https://github.com/rstudio/rmarkdown, https://pkgs.rstudio.com/rmarkdown/", + "BugReports": "https://github.com/rstudio/rmarkdown/issues", + "Depends": [ + "R (>= 3.0)" + ], + "Imports": [ + "bslib (>= 0.2.5.1)", + "evaluate (>= 0.13)", + "fontawesome (>= 0.5.0)", + "htmltools (>= 0.5.1)", + "jquerylib", + "jsonlite", + "knitr (>= 1.43)", + "methods", + "tinytex (>= 0.31)", + "tools", + "utils", + "xfun (>= 0.36)", + "yaml (>= 2.1.19)" + ], + "Suggests": [ + "digest", + "dygraphs", + "fs", + "rsconnect", + "downlit (>= 0.4.0)", + "katex (>= 1.4.0)", + "sass (>= 0.4.0)", + "shiny (>= 1.6.0)", + "testthat (>= 3.0.3)", + "tibble", + "vctrs", + "cleanrmd", + "withr (>= 2.4.2)", + "xml2" + ], + "VignetteBuilder": "knitr", + "Config/Needs/website": "rstudio/quillt, pkgdown", + "Config/testthat/edition": "3", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.2", + "SystemRequirements": "pandoc (>= 1.14) - http://pandoc.org", + "NeedsCompilation": "no", + "Author": "JJ Allaire [aut], Yihui Xie [aut, cre] 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[ctb, cph] (ioslides library), Dave Raggett [ctb] (slidy library), W3C [cph] (slidy library), Dave Gandy [ctb, cph] (Font-Awesome), Ben Sperry [ctb] (Ionicons), Drifty [cph] (Ionicons), Aidan Lister [ctb, cph] (jQuery StickyTabs), Benct Philip Jonsson [ctb, cph] (pagebreak Lua filter), Albert Krewinkel [ctb, cph] (pagebreak Lua filter)", + "Maintainer": "Yihui Xie <xie@yihui.name>", + "Repository": "CRAN" + }, + "rpart": { + "Package": "rpart", + "Version": "4.1.24", + "Source": "Repository", + "Priority": "recommended", + "Date": "2025-01-06", + "Authors@R": "c(person(\"Terry\", \"Therneau\", role = \"aut\", email = \"therneau@mayo.edu\"), person(\"Beth\", \"Atkinson\", role = c(\"aut\", \"cre\"), email = \"atkinson@mayo.edu\"), person(\"Brian\", \"Ripley\", role = \"trl\", email = \"ripley@stats.ox.ac.uk\", comment = \"producer of the initial R port, maintainer 1999-2017\"))", + "Description": "Recursive partitioning for classification, regression and survival trees. An implementation of most of the functionality of the 1984 book by Breiman, Friedman, Olshen and Stone.", + "Title": "Recursive Partitioning and Regression Trees", + "Depends": [ + "R (>= 2.15.0)", + "graphics", + "stats", + "grDevices" + ], + "Suggests": [ + "survival" + ], + "License": "GPL-2 | GPL-3", + "LazyData": "yes", + "ByteCompile": "yes", + "NeedsCompilation": "yes", + "Author": "Terry Therneau [aut], Beth Atkinson [aut, cre], Brian Ripley [trl] (producer of the initial R port, maintainer 1999-2017)", + "Maintainer": "Beth Atkinson <atkinson@mayo.edu>", + "Repository": "CRAN", + "URL": "https://github.com/bethatkinson/rpart, https://cran.r-project.org/package=rpart", + "BugReports": "https://github.com/bethatkinson/rpart/issues" + }, + "rprojroot": { + "Package": "rprojroot", + "Version": "2.0.4", + "Source": "Repository", + "Title": "Finding Files in Project Subdirectories", + "Authors@R": "person(given = \"Kirill\", family = \"M\\u00fcller\", role = c(\"aut\", \"cre\"), email = \"kirill@cynkra.com\", comment = c(ORCID = \"0000-0002-1416-3412\"))", + "Description": "Robust, reliable and flexible paths to files below a project root. The 'root' of a project is defined as a directory that matches a certain criterion, e.g., it contains a certain regular file.", + "License": "MIT + file LICENSE", + "URL": "https://rprojroot.r-lib.org/, https://github.com/r-lib/rprojroot", + "BugReports": "https://github.com/r-lib/rprojroot/issues", + "Depends": [ + "R (>= 3.0.0)" + ], + "Suggests": [ + "covr", + "knitr", + "lifecycle", + "mockr", + "rlang", + "rmarkdown", + "testthat (>= 3.0.0)", + "withr" + ], + "VignetteBuilder": "knitr", + "Config/testthat/edition": "3", + "Encoding": "UTF-8", + "RoxygenNote": "7.2.3", + "NeedsCompilation": "no", + "Author": "Kirill Müller [aut, cre] (<https://orcid.org/0000-0002-1416-3412>)", + "Maintainer": "Kirill Müller <kirill@cynkra.com>", + "Repository": "CRAN" + }, + "rstudioapi": { + "Package": "rstudioapi", + "Version": "0.17.1", + "Source": "Repository", + "Title": "Safely Access the RStudio API", + "Description": "Access the RStudio API (if available) and provide informative error messages when it's not.", + "Authors@R": "c( person(\"Kevin\", \"Ushey\", role = c(\"aut\", \"cre\"), email = \"kevin@rstudio.com\"), person(\"JJ\", \"Allaire\", role = c(\"aut\"), email = \"jj@posit.co\"), person(\"Hadley\", \"Wickham\", role = c(\"aut\"), email = \"hadley@posit.co\"), person(\"Gary\", \"Ritchie\", role = c(\"aut\"), email = \"gary@posit.co\"), person(family = \"RStudio\", role = \"cph\") )", + "Maintainer": "Kevin Ushey <kevin@rstudio.com>", + "License": "MIT + file LICENSE", + "URL": "https://rstudio.github.io/rstudioapi/, https://github.com/rstudio/rstudioapi", + "BugReports": "https://github.com/rstudio/rstudioapi/issues", + "RoxygenNote": "7.3.2", + "Suggests": [ + "testthat", + "knitr", + "rmarkdown", + "clipr", + "covr" + ], + "VignetteBuilder": "knitr", + "Encoding": "UTF-8", + "NeedsCompilation": "no", + "Author": "Kevin Ushey [aut, cre], JJ Allaire [aut], Hadley Wickham [aut], Gary Ritchie [aut], RStudio [cph]", + "Repository": "CRAN" + }, + "sass": { + "Package": "sass", + "Version": "0.4.9", + "Source": "Repository", + "Type": "Package", + "Title": "Syntactically Awesome Style Sheets ('Sass')", + "Description": "An 'SCSS' compiler, powered by the 'LibSass' library. With this, R developers can use variables, inheritance, and functions to generate dynamic style sheets. The package uses the 'Sass CSS' extension language, which is stable, powerful, and CSS compatible.", + "Authors@R": "c( person(\"Joe\", \"Cheng\", , \"joe@rstudio.com\", \"aut\"), person(\"Timothy\", \"Mastny\", , \"tim.mastny@gmail.com\", \"aut\"), person(\"Richard\", \"Iannone\", , \"rich@rstudio.com\", \"aut\", comment = c(ORCID = \"0000-0003-3925-190X\")), person(\"Barret\", \"Schloerke\", , \"barret@rstudio.com\", \"aut\", comment = c(ORCID = \"0000-0001-9986-114X\")), person(\"Carson\", \"Sievert\", , \"carson@rstudio.com\", c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-4958-2844\")), person(\"Christophe\", \"Dervieux\", , \"cderv@rstudio.com\", c(\"ctb\"), comment = c(ORCID = \"0000-0003-4474-2498\")), person(family = \"RStudio\", role = c(\"cph\", \"fnd\")), person(family = \"Sass Open Source Foundation\", role = c(\"ctb\", \"cph\"), comment = \"LibSass library\"), person(\"Greter\", \"Marcel\", role = c(\"ctb\", \"cph\"), comment = \"LibSass library\"), person(\"Mifsud\", \"Michael\", role = c(\"ctb\", \"cph\"), comment = \"LibSass library\"), person(\"Hampton\", \"Catlin\", role = c(\"ctb\", \"cph\"), comment = \"LibSass library\"), person(\"Natalie\", \"Weizenbaum\", role = c(\"ctb\", \"cph\"), comment = \"LibSass library\"), person(\"Chris\", \"Eppstein\", role = c(\"ctb\", \"cph\"), comment = \"LibSass library\"), person(\"Adams\", \"Joseph\", role = c(\"ctb\", \"cph\"), comment = \"json.cpp\"), person(\"Trifunovic\", \"Nemanja\", role = c(\"ctb\", \"cph\"), comment = \"utf8.h\") )", + "License": "MIT + file LICENSE", + "URL": "https://rstudio.github.io/sass/, https://github.com/rstudio/sass", + "BugReports": "https://github.com/rstudio/sass/issues", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.1", + "SystemRequirements": "GNU make", + "Imports": [ + "fs (>= 1.2.4)", + "rlang (>= 0.4.10)", + "htmltools (>= 0.5.1)", + "R6", + "rappdirs" + ], + "Suggests": [ + "testthat", + "knitr", + "rmarkdown", + "withr", + "shiny", + "curl" + ], + "VignetteBuilder": "knitr", + "Config/testthat/edition": "3", + "NeedsCompilation": "yes", + "Author": "Joe Cheng [aut], Timothy Mastny [aut], Richard Iannone [aut] (<https://orcid.org/0000-0003-3925-190X>), Barret Schloerke [aut] (<https://orcid.org/0000-0001-9986-114X>), Carson Sievert [aut, cre] (<https://orcid.org/0000-0002-4958-2844>), Christophe Dervieux [ctb] (<https://orcid.org/0000-0003-4474-2498>), RStudio [cph, fnd], Sass Open Source Foundation [ctb, cph] (LibSass library), Greter Marcel [ctb, cph] (LibSass library), Mifsud Michael [ctb, cph] (LibSass library), Hampton Catlin [ctb, cph] (LibSass library), Natalie Weizenbaum [ctb, cph] (LibSass library), Chris Eppstein [ctb, cph] (LibSass library), Adams Joseph [ctb, cph] (json.cpp), Trifunovic Nemanja [ctb, cph] (utf8.h)", + "Maintainer": "Carson Sievert <carson@rstudio.com>", + "Repository": "CRAN" + }, + "scales": { + "Package": "scales", + "Version": "1.3.0", + "Source": "Repository", + "Title": "Scale Functions for 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"Prototype your shiny apps quickly with these Lorem-Ipsum-like Helpers.", + "License": "MIT + file LICENSE", + "URL": "https://github.com/Thinkr-open/shinipsum", + "BugReports": "https://github.com/Thinkr-open/shinipsum/issues", + "Depends": [ + "R (>= 2.10)" + ], + "Imports": [ + "attempt", + "datasets", + "DT", + "dygraphs", + "ggplot2 (>= 3.0.0)", + "magrittr", + "plotly", + "stats", + "utils" + ], + "Suggests": [ + "testthat" + ], + "Encoding": "UTF-8", + "LazyData": "true", + "RoxygenNote": "7.2.3", + "NeedsCompilation": "no", + "Author": "Colin Fay [cre, aut] (<https://orcid.org/0000-0001-7343-1846>), Sebastien Rochette [aut] (<https://orcid.org/0000-0002-1565-9313>), ThinkR [cph, fnd]", + "Maintainer": "Colin Fay <contact@colinfay.me>", + "Repository": "CRAN" + }, + "shiny": { + "Package": "shiny", + "Version": "1.10.0", + "Source": "Repository", + "Type": "Package", + "Title": "Web Application Framework for R", + "Authors@R": "c( person(\"Winston\", \"Chang\", role = c(\"aut\", \"cre\"), email = \"winston@posit.co\", comment = c(ORCID = \"0000-0002-1576-2126\")), person(\"Joe\", \"Cheng\", role = \"aut\", email = \"joe@posit.co\"), person(\"JJ\", \"Allaire\", role = \"aut\", email = \"jj@posit.co\"), person(\"Carson\", \"Sievert\", role = \"aut\", email = \"carson@posit.co\", comment = c(ORCID = \"0000-0002-4958-2844\")), person(\"Barret\", \"Schloerke\", role = \"aut\", email = \"barret@posit.co\", comment = c(ORCID = \"0000-0001-9986-114X\")), person(\"Yihui\", \"Xie\", role = \"aut\", email = \"yihui@posit.co\"), person(\"Jeff\", \"Allen\", role = \"aut\"), person(\"Jonathan\", \"McPherson\", role = \"aut\", email = \"jonathan@posit.co\"), person(\"Alan\", \"Dipert\", role = \"aut\"), person(\"Barbara\", \"Borges\", role = \"aut\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")), person(family = \"jQuery Foundation\", role = \"cph\", comment = \"jQuery library and jQuery UI library\"), person(family = \"jQuery contributors\", role = c(\"ctb\", \"cph\"), comment = \"jQuery library; authors listed in inst/www/shared/jquery-AUTHORS.txt\"), person(family = \"jQuery UI contributors\", role = c(\"ctb\", \"cph\"), comment = \"jQuery UI library; authors listed in inst/www/shared/jqueryui/AUTHORS.txt\"), person(\"Mark\", \"Otto\", role = \"ctb\", comment = \"Bootstrap library\"), person(\"Jacob\", \"Thornton\", role = \"ctb\", comment = \"Bootstrap library\"), person(family = \"Bootstrap contributors\", role = \"ctb\", comment = \"Bootstrap library\"), person(family = \"Twitter, Inc\", role = \"cph\", comment = \"Bootstrap library\"), person(\"Prem Nawaz\", \"Khan\", role = \"ctb\", comment = \"Bootstrap accessibility plugin\"), person(\"Victor\", \"Tsaran\", role = \"ctb\", comment = \"Bootstrap accessibility plugin\"), person(\"Dennis\", \"Lembree\", role = \"ctb\", comment = \"Bootstrap accessibility plugin\"), person(\"Srinivasu\", \"Chakravarthula\", role = \"ctb\", comment = \"Bootstrap accessibility plugin\"), 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'AdminLTE2' is a free 'Bootstrap 3' dashboard template available at <https://adminlte.io>. Customize boxes, add timelines and a lot more.", + "License": "GPL (>= 2) | file LICENSE", + "Imports": [ + "shiny", + "htmltools", + "shinydashboard", + "fresh", + "waiter (>= 0.2.3)", + "lifecycle" + ], + "Suggests": [ + "styler (>= 1.2.0)", + "shinyAce", + "shinyWidgets", + "shinyEffects", + "shinyjqui", + "knitr", + "rmarkdown", + "jsonlite", + "bslib" + ], + "URL": "https://github.com/RinteRface/shinydashboardPlus, https://shinydashboardPlus.rinterface.com/", + "BugReports": "https://github.com/RinteRface/shinydashboardPlus/issues", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.2", + "VignetteBuilder": "knitr", + "RdMacros": "lifecycle", + "NeedsCompilation": "no", + "Author": "David Granjon [aut, cre], RinteRface [cph], Almasaeed Studio [ctb, cph] (AdminLTE2 theme for Bootstrap 3), Guang Yang [ctb, cph] (ygdashboard original template), Winston Chang [ctb, cph] (Functions from shinydashboard), Victor Perrier [ctb] (improved the shinydashboardPlusGallery)", + "Repository": "CRAN" + }, + "shinyjs": { + "Package": "shinyjs", + "Version": "2.1.0", + "Source": "Repository", + "Title": "Easily Improve the User Experience of Your Shiny Apps in Seconds", + "Authors@R": "person(\"Dean\", \"Attali\", email = \"daattali@gmail.com\", role = c(\"aut\", \"cre\"), comment= c(ORCID=\"0000-0002-5645-3493\"))", + "Description": "Perform common useful JavaScript operations in Shiny apps that will greatly improve your apps without having to know any JavaScript. 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'shinyjs' can also be used to easily call your own custom JavaScript functions from R.", + "URL": "https://deanattali.com/shinyjs/", + "BugReports": "https://github.com/daattali/shinyjs/issues", + "Depends": [ + "R (>= 3.1.0)" + ], + "Imports": [ + "digest (>= 0.6.8)", + "jsonlite", + "shiny (>= 1.0.0)" + ], + "Suggests": [ + "htmltools (>= 0.2.9)", + "knitr (>= 1.7)", + "rmarkdown", + "shinyAce", + "shinydisconnect", + "testthat (>= 0.9.1)" + ], + "License": "MIT + file LICENSE", + "VignetteBuilder": "knitr", + "RoxygenNote": "7.1.1", + "Encoding": "UTF-8", + "NeedsCompilation": "no", + "Author": "Dean Attali [aut, cre] (<https://orcid.org/0000-0002-5645-3493>)", + "Maintainer": "Dean Attali <daattali@gmail.com>", + "Repository": "CRAN" + }, + "shinytoastr": { + "Package": "shinytoastr", + "Version": "2.2.0", + "Source": "Repository", + "Title": "Notifications from 'Shiny'", + "Author": "John Papa, Tim Ferrell, Hans Fjällemark, Gábor Csárdi", + "Maintainer": "Gábor Csárdi <csardi.gabor@gmail.com>", + "Description": "Browser notifications in 'Shiny' apps, using 'toastr': <https://github.com/CodeSeven/toastr#readme>.", + "License": "MIT + file LICENSE", + "URL": "https://github.com/gaborcsardi/shinytoastr", + "BugReports": "https://github.com/gaborcsardi/shinytoastr/issues", + "Imports": [ + "shiny" + ], + "RoxygenNote": "5.0.1", + "Encoding": "UTF-8", + "NeedsCompilation": "no", + "Repository": "CRAN" + }, + "sourcetools": { + "Package": "sourcetools", + "Version": "0.1.7-1", + "Source": "Repository", + "Type": "Package", + "Title": "Tools for Reading, Tokenizing and Parsing R Code", + "Author": "Kevin Ushey", + "Maintainer": "Kevin Ushey <kevinushey@gmail.com>", + "Description": "Tools for the reading and tokenization of R code. 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It makes it easy to implement select-like functions in your own packages in a way that is consistent with other 'tidyverse' interfaces for selection.", + "License": "MIT + file LICENSE", + "URL": "https://tidyselect.r-lib.org, https://github.com/r-lib/tidyselect", + "BugReports": "https://github.com/r-lib/tidyselect/issues", + "Depends": [ + "R (>= 3.4)" + ], + "Imports": [ + "cli (>= 3.3.0)", + "glue (>= 1.3.0)", + "lifecycle (>= 1.0.3)", + "rlang (>= 1.0.4)", + "vctrs (>= 0.5.2)", + "withr" + ], + "Suggests": [ + "covr", + "crayon", + "dplyr", + "knitr", + "magrittr", + "rmarkdown", + "stringr", + "testthat (>= 3.1.1)", + "tibble (>= 2.1.3)" + ], + "VignetteBuilder": "knitr", + "ByteCompile": "true", + "Config/testthat/edition": "3", + "Config/Needs/website": "tidyverse/tidytemplate", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.0.9000", + "NeedsCompilation": "yes", + "Author": "Lionel Henry [aut, cre], Hadley Wickham [aut], Posit Software, PBC [cph, fnd]", + "Maintainer": "Lionel Henry <lionel@posit.co>", + "Repository": "CRAN" + }, + "timechange": { + "Package": "timechange", + "Version": "0.3.0", + "Source": "Repository", + "Title": "Efficient Manipulation of Date-Times", + "Authors@R": "c(person(\"Vitalie\", \"Spinu\", email = \"spinuvit@gmail.com\", role = c(\"aut\", \"cre\")), person(\"Google Inc.\", role = c(\"ctb\", \"cph\")))", + "Description": "Efficient routines for manipulation of date-time objects while accounting for time-zones and daylight saving times. 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This package also contains helper functions to compile 'LaTeX' documents, and install missing 'LaTeX' packages automatically.", + "Imports": [ + "xfun (>= 0.48)" + ], + "Suggests": [ + "testit", + "rstudioapi" + ], + "License": "MIT + file LICENSE", + "URL": "https://github.com/rstudio/tinytex", + "BugReports": "https://github.com/rstudio/tinytex/issues", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.2", + "NeedsCompilation": "no", + "Author": "Yihui Xie [aut, cre, cph] (<https://orcid.org/0000-0003-0645-5666>), Posit Software, PBC [cph, fnd], Christophe Dervieux [ctb] (<https://orcid.org/0000-0003-4474-2498>), Devon Ryan [ctb] (<https://orcid.org/0000-0002-8549-0971>), Ethan Heinzen [ctb], Fernando Cagua [ctb]", + "Maintainer": "Yihui Xie <xie@yihui.name>", + "Repository": "CRAN" + }, + "utf8": { + "Package": "utf8", + "Version": "1.2.4", + "Source": "Repository", + "Title": "Unicode Text Processing", + "Authors@R": "c(person(given = c(\"Patrick\", \"O.\"), family = \"Perry\", role = c(\"aut\", \"cph\")), person(given = \"Kirill\", family = \"M\\u00fcller\", role = \"cre\", email = \"kirill@cynkra.com\"), person(given = \"Unicode, Inc.\", role = c(\"cph\", \"dtc\"), comment = \"Unicode Character Database\"))", + "Description": "Process and print 'UTF-8' encoded international text (Unicode). Input, validate, normalize, encode, format, and display.", + "License": "Apache License (== 2.0) | file LICENSE", + "URL": "https://ptrckprry.com/r-utf8/, https://github.com/patperry/r-utf8", + "BugReports": "https://github.com/patperry/r-utf8/issues", + "Depends": [ + "R (>= 2.10)" + ], + "Suggests": [ + "cli", + "covr", + "knitr", + "rlang", + "rmarkdown", + "testthat (>= 3.0.0)", + "withr" + ], + "VignetteBuilder": "knitr, rmarkdown", + "Config/testthat/edition": "3", + "Encoding": "UTF-8", + "RoxygenNote": "7.2.3", + "NeedsCompilation": "yes", + "Author": "Patrick O. Perry [aut, cph], Kirill Müller [cre], Unicode, Inc. [cph, dtc] (Unicode Character Database)", + "Maintainer": "Kirill Müller <kirill@cynkra.com>", + "Repository": "CRAN" + }, + "vctrs": { + "Package": "vctrs", + "Version": "0.6.5", + "Source": "Repository", + "Title": "Vector Helpers", + "Authors@R": "c( person(\"Hadley\", \"Wickham\", , \"hadley@posit.co\", role = \"aut\"), person(\"Lionel\", \"Henry\", , \"lionel@posit.co\", role = \"aut\"), person(\"Davis\", \"Vaughan\", , \"davis@posit.co\", role = c(\"aut\", \"cre\")), person(\"data.table team\", role = \"cph\", comment = \"Radix sort based on data.table's forder() and their contribution to R's order()\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", + "Description": "Defines new notions of prototype and size that are used to provide tools for consistent and well-founded type-coercion and size-recycling, and are in turn connected to ideas of type- and size-stability useful for analysing function interfaces.", + "License": "MIT + file LICENSE", + "URL": "https://vctrs.r-lib.org/, https://github.com/r-lib/vctrs", + "BugReports": "https://github.com/r-lib/vctrs/issues", + "Depends": [ + "R (>= 3.5.0)" + ], + "Imports": [ + "cli (>= 3.4.0)", + "glue", + "lifecycle (>= 1.0.3)", + "rlang (>= 1.1.0)" + ], + "Suggests": [ + "bit64", + "covr", + "crayon", + "dplyr (>= 0.8.5)", + "generics", + "knitr", + "pillar (>= 1.4.4)", + "pkgdown (>= 2.0.1)", + "rmarkdown", + "testthat (>= 3.0.0)", + "tibble (>= 3.1.3)", + "waldo (>= 0.2.0)", + "withr", + "xml2", + "zeallot" + ], + "VignetteBuilder": "knitr", + "Config/Needs/website": "tidyverse/tidytemplate", + "Config/testthat/edition": "3", + "Encoding": "UTF-8", + "Language": "en-GB", + "RoxygenNote": "7.2.3", + "NeedsCompilation": "yes", + "Author": "Hadley Wickham [aut], Lionel Henry [aut], Davis Vaughan [aut, cre], data.table team [cph] (Radix sort based on data.table's forder() and their contribution to R's order()), Posit Software, PBC [cph, fnd]", + "Maintainer": "Davis Vaughan <davis@posit.co>", + "Repository": "CRAN" + }, + "viridis": { + "Package": "viridis", + "Version": "0.6.5", + "Source": "Repository", + "Type": "Package", + "Title": "Colorblind-Friendly Color Maps for R", + "Date": "2024-01-28", + "Authors@R": "c( person(\"Simon\", \"Garnier\", email = \"garnier@njit.edu\", role = c(\"aut\", \"cre\")), person(\"Noam\", \"Ross\", email = \"noam.ross@gmail.com\", role = c(\"ctb\", \"cph\")), person(\"Bob\", \"Rudis\", email = \"bob@rud.is\", role = c(\"ctb\", \"cph\")), person(\"Marco\", \"Sciaini\", email = \"sciaini.marco@gmail.com\", role = c(\"ctb\", \"cph\")), person(\"Antônio Pedro\", \"Camargo\", role = c(\"ctb\", \"cph\")), person(\"Cédric\", \"Scherer\", email = \"scherer@izw-berlin.de\", role = c(\"ctb\", \"cph\")) )", + "Maintainer": "Simon Garnier <garnier@njit.edu>", + "Description": "Color maps designed to improve graph readability for readers with common forms of color blindness and/or color vision deficiency. The color maps are also perceptually-uniform, both in regular form and also when converted to black-and-white for printing. This package also contains 'ggplot2' bindings for discrete and continuous color and fill scales. A lean version of the package called 'viridisLite' that does not include the 'ggplot2' bindings can be found at <https://cran.r-project.org/package=viridisLite>.", + "License": "MIT + file LICENSE", + "Encoding": "UTF-8", + "Depends": [ + "R (>= 2.10)", + "viridisLite (>= 0.4.0)" + ], + "Imports": [ + "ggplot2 (>= 1.0.1)", + "gridExtra" + ], + "Suggests": [ + "hexbin (>= 1.27.0)", + "scales", + "MASS", + "knitr", + "dichromat", + "colorspace", + "httr", + "mapproj", + "vdiffr", + "svglite (>= 1.2.0)", + "testthat", + "covr", + "rmarkdown", + "maps", + "terra" + ], + "LazyData": "true", + "VignetteBuilder": "knitr", + "URL": "https://sjmgarnier.github.io/viridis/, https://github.com/sjmgarnier/viridis/", + "BugReports": "https://github.com/sjmgarnier/viridis/issues", + "RoxygenNote": "7.3.1", + "NeedsCompilation": "no", + "Author": "Simon Garnier [aut, cre], Noam Ross [ctb, cph], Bob Rudis [ctb, cph], Marco Sciaini [ctb, cph], Antônio Pedro Camargo [ctb, cph], Cédric Scherer [ctb, cph]", + "Repository": "CRAN" + }, + "viridisLite": { + "Package": "viridisLite", + "Version": "0.4.2", + "Source": "Repository", + "Type": "Package", + "Title": "Colorblind-Friendly Color Maps (Lite Version)", + "Date": "2023-05-02", + "Authors@R": "c( person(\"Simon\", \"Garnier\", email = \"garnier@njit.edu\", role = c(\"aut\", \"cre\")), person(\"Noam\", \"Ross\", email = \"noam.ross@gmail.com\", role = c(\"ctb\", \"cph\")), person(\"Bob\", \"Rudis\", email = \"bob@rud.is\", role = c(\"ctb\", \"cph\")), person(\"Marco\", \"Sciaini\", email = \"sciaini.marco@gmail.com\", role = c(\"ctb\", \"cph\")), person(\"Antônio Pedro\", \"Camargo\", role = c(\"ctb\", \"cph\")), person(\"Cédric\", \"Scherer\", email = \"scherer@izw-berlin.de\", role = c(\"ctb\", \"cph\")) )", + "Maintainer": "Simon Garnier <garnier@njit.edu>", + "Description": "Color maps designed to improve graph readability for readers with common forms of color blindness and/or color vision deficiency. The color maps are also perceptually-uniform, both in regular form and also when converted to black-and-white for printing. This is the 'lite' version of the 'viridis' package that also contains 'ggplot2' bindings for discrete and continuous color and fill scales and can be found at <https://cran.r-project.org/package=viridis>.", + "License": "MIT + file LICENSE", + "Encoding": "UTF-8", + "Depends": [ + "R (>= 2.10)" + ], + "Suggests": [ + "hexbin (>= 1.27.0)", + "ggplot2 (>= 1.0.1)", + "testthat", + "covr" + ], + "URL": "https://sjmgarnier.github.io/viridisLite/, https://github.com/sjmgarnier/viridisLite/", + "BugReports": "https://github.com/sjmgarnier/viridisLite/issues/", + "RoxygenNote": "7.2.3", + "NeedsCompilation": "no", + "Author": "Simon Garnier [aut, cre], Noam Ross [ctb, cph], Bob Rudis [ctb, cph], Marco Sciaini [ctb, cph], Antônio Pedro Camargo [ctb, cph], Cédric Scherer [ctb, cph]", + "Repository": "CRAN" + }, + "waiter": { + "Package": "waiter", + "Version": "0.2.5", + "Source": "Repository", + "Title": "Loading Screen for 'Shiny'", + "Date": "2022-01-02", + "Authors@R": "c( person(given = \"John\", family = \"Coene\", role = c(\"aut\", \"cre\"), email = \"jcoenep@gmail.com\"), person(given = \"Jinhwan\", family = \"Kim\", role = \"ctb\", email = 'hwanistic@gmail.com'), person(given = \"Victor\", family = \"Granda\", role = c(\"ctb\"), email = \"victorgrandagarcia@gmail.com\", comment = c(ORCID = \"0000-0002-0469-1991\")))", + "Description": "Full screen and partial loading screens for 'Shiny' with spinners, progress bars, and notifications.", + "License": "MIT + file LICENSE", + "URL": "https://waiter.john-coene.com/, https://github.com/JohnCoene/waiter", + "BugReports": "https://github.com/JohnCoene/waiter/issues", + "Encoding": "UTF-8", + "Imports": [ + "R6", + "shiny", + "htmltools" + ], + "RoxygenNote": "7.1.2", + "Suggests": [ + "httr", + "knitr", + "packer", + "rmarkdown" + ], + "VignetteBuilder": "knitr", + "NeedsCompilation": "no", + "Author": "John Coene [aut, cre], Jinhwan Kim [ctb], Victor Granda [ctb] (<https://orcid.org/0000-0002-0469-1991>)", + "Maintainer": "John Coene <jcoenep@gmail.com>", + "Repository": "CRAN" + }, + "withr": { + "Package": "withr", + "Version": "3.0.2", + "Source": "Repository", + "Title": "Run Code 'With' Temporarily Modified Global State", + "Authors@R": "c( person(\"Jim\", \"Hester\", role = \"aut\"), person(\"Lionel\", \"Henry\", , \"lionel@posit.co\", role = c(\"aut\", \"cre\")), person(\"Kirill\", \"Müller\", , \"krlmlr+r@mailbox.org\", role = \"aut\"), person(\"Kevin\", \"Ushey\", , \"kevinushey@gmail.com\", role = \"aut\"), person(\"Hadley\", \"Wickham\", , \"hadley@posit.co\", role = \"aut\"), person(\"Winston\", \"Chang\", role = \"aut\"), person(\"Jennifer\", \"Bryan\", role = \"ctb\"), person(\"Richard\", \"Cotton\", role = \"ctb\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", + "Description": "A set of functions to run code 'with' safely and temporarily modified global state. Many of these functions were originally a part of the 'devtools' package, this provides a simple package with limited dependencies to provide access to these functions.", + "License": "MIT + file LICENSE", + "URL": "https://withr.r-lib.org, https://github.com/r-lib/withr#readme", + "BugReports": "https://github.com/r-lib/withr/issues", + "Depends": [ + "R (>= 3.6.0)" + ], + "Imports": [ + "graphics", + "grDevices" + ], + "Suggests": [ + "callr", + "DBI", + "knitr", + "methods", + "rlang", + "rmarkdown (>= 2.12)", + "RSQLite", + "testthat (>= 3.0.0)" + ], + "VignetteBuilder": "knitr", + "Config/Needs/website": "tidyverse/tidytemplate", + "Config/testthat/edition": "3", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.2", + "Collate": "'aaa.R' 'collate.R' 'connection.R' 'db.R' 'defer-exit.R' 'standalone-defer.R' 'defer.R' 'devices.R' 'local_.R' 'with_.R' 'dir.R' 'env.R' 'file.R' 'language.R' 'libpaths.R' 'locale.R' 'makevars.R' 'namespace.R' 'options.R' 'par.R' 'path.R' 'rng.R' 'seed.R' 'wrap.R' 'sink.R' 'tempfile.R' 'timezone.R' 'torture.R' 'utils.R' 'with.R'", + "NeedsCompilation": "no", + "Author": "Jim Hester [aut], Lionel Henry [aut, cre], Kirill Müller [aut], Kevin Ushey [aut], Hadley Wickham [aut], Winston Chang [aut], Jennifer Bryan [ctb], Richard Cotton [ctb], Posit Software, PBC [cph, fnd]", + "Maintainer": "Lionel Henry <lionel@posit.co>", + "Repository": "RSPM" + }, + "xfun": { + "Package": "xfun", + "Version": "0.51", + "Source": "Repository", + "Type": "Package", + "Title": "Supporting Functions for Packages Maintained by 'Yihui Xie'", + "Authors@R": "c( person(\"Yihui\", \"Xie\", role = c(\"aut\", \"cre\", \"cph\"), email = \"xie@yihui.name\", comment = c(ORCID = \"0000-0003-0645-5666\", URL = \"https://yihui.org\")), person(\"Wush\", \"Wu\", role = \"ctb\"), person(\"Daijiang\", \"Li\", role = \"ctb\"), person(\"Xianying\", \"Tan\", role = \"ctb\"), person(\"Salim\", \"Brüggemann\", role = \"ctb\", email = \"salim-b@pm.me\", comment = c(ORCID = \"0000-0002-5329-5987\")), person(\"Christophe\", \"Dervieux\", role = \"ctb\"), person() )", + "Description": "Miscellaneous functions commonly used in other packages maintained by 'Yihui Xie'.", + "Depends": [ + "R (>= 3.2.0)" + ], + "Imports": [ + "grDevices", + "stats", + "tools" + ], + "Suggests": [ + "testit", + "parallel", + "codetools", + "methods", + "rstudioapi", + "tinytex (>= 0.30)", + "mime", + "litedown (>= 0.4)", + "commonmark", + "knitr (>= 1.47)", + "remotes", + "pak", + "rhub", + "renv", + "curl", + "xml2", + "jsonlite", + "magick", + "yaml", + "qs", + "rmarkdown" + ], + "License": "MIT + file LICENSE", + "URL": "https://github.com/yihui/xfun", + "BugReports": "https://github.com/yihui/xfun/issues", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.2", + "VignetteBuilder": "litedown", + "NeedsCompilation": "yes", + "Author": "Yihui Xie [aut, cre, cph] (<https://orcid.org/0000-0003-0645-5666>, https://yihui.org), Wush Wu [ctb], Daijiang Li [ctb], Xianying Tan [ctb], Salim Brüggemann [ctb] (<https://orcid.org/0000-0002-5329-5987>), Christophe Dervieux [ctb]", + "Maintainer": "Yihui Xie <xie@yihui.name>", + "Repository": "CRAN" + }, + "xtable": { + "Package": "xtable", + "Version": "1.8-4", + "Source": "Repository", + "Date": "2019-04-08", + "Title": "Export Tables to LaTeX or HTML", + "Authors@R": "c(person(\"David B.\", \"Dahl\", role=\"aut\"), person(\"David\", \"Scott\", role=c(\"aut\",\"cre\"), email=\"d.scott@auckland.ac.nz\"), person(\"Charles\", \"Roosen\", role=\"aut\"), person(\"Arni\", \"Magnusson\", role=\"aut\"), person(\"Jonathan\", \"Swinton\", role=\"aut\"), person(\"Ajay\", \"Shah\", role=\"ctb\"), person(\"Arne\", \"Henningsen\", role=\"ctb\"), person(\"Benno\", \"Puetz\", role=\"ctb\"), person(\"Bernhard\", \"Pfaff\", role=\"ctb\"), person(\"Claudio\", \"Agostinelli\", role=\"ctb\"), person(\"Claudius\", \"Loehnert\", role=\"ctb\"), person(\"David\", \"Mitchell\", role=\"ctb\"), person(\"David\", \"Whiting\", role=\"ctb\"), person(\"Fernando da\", \"Rosa\", role=\"ctb\"), person(\"Guido\", \"Gay\", role=\"ctb\"), person(\"Guido\", \"Schulz\", role=\"ctb\"), person(\"Ian\", \"Fellows\", role=\"ctb\"), person(\"Jeff\", \"Laake\", role=\"ctb\"), person(\"John\", \"Walker\", role=\"ctb\"), person(\"Jun\", \"Yan\", role=\"ctb\"), person(\"Liviu\", \"Andronic\", role=\"ctb\"), person(\"Markus\", \"Loecher\", role=\"ctb\"), person(\"Martin\", \"Gubri\", role=\"ctb\"), person(\"Matthieu\", \"Stigler\", role=\"ctb\"), person(\"Robert\", \"Castelo\", role=\"ctb\"), person(\"Seth\", \"Falcon\", role=\"ctb\"), person(\"Stefan\", \"Edwards\", role=\"ctb\"), person(\"Sven\", \"Garbade\", role=\"ctb\"), person(\"Uwe\", \"Ligges\", role=\"ctb\"))", + "Maintainer": "David Scott <d.scott@auckland.ac.nz>", + "Imports": [ + "stats", + "utils" + ], + "Suggests": [ + "knitr", + "plm", + "zoo", + "survival" + ], + "VignetteBuilder": "knitr", + "Description": "Coerce data to LaTeX and HTML tables.", + "URL": "http://xtable.r-forge.r-project.org/", + "Depends": [ + "R (>= 2.10.0)" + ], + "License": "GPL (>= 2)", + "Repository": "CRAN", + "NeedsCompilation": "no", + "Author": "David B. Dahl [aut], David Scott [aut, cre], Charles Roosen [aut], Arni Magnusson [aut], Jonathan Swinton [aut], Ajay Shah [ctb], Arne Henningsen [ctb], Benno Puetz [ctb], Bernhard Pfaff [ctb], Claudio Agostinelli [ctb], Claudius Loehnert [ctb], David Mitchell [ctb], David Whiting [ctb], Fernando da Rosa [ctb], Guido Gay [ctb], Guido Schulz [ctb], Ian Fellows [ctb], Jeff Laake [ctb], John Walker [ctb], Jun Yan [ctb], Liviu Andronic [ctb], Markus Loecher [ctb], Martin Gubri [ctb], Matthieu Stigler [ctb], Robert Castelo [ctb], Seth Falcon [ctb], Stefan Edwards [ctb], Sven Garbade [ctb], Uwe Ligges [ctb]" + }, + "xts": { + "Package": "xts", + "Version": "0.14.1", + "Source": "Repository", + "Type": "Package", + "Title": "eXtensible Time Series", + "Authors@R": "c( person(given=c(\"Jeffrey\",\"A.\"), family=\"Ryan\", role=c(\"aut\",\"cph\")), person(given=c(\"Joshua\",\"M.\"), family=\"Ulrich\", role=c(\"cre\",\"aut\"), email=\"josh.m.ulrich@gmail.com\"), person(given=\"Ross\", family=\"Bennett\", role=\"ctb\"), person(given=\"Corwin\", family=\"Joy\", role=\"ctb\") )", + "Depends": [ + "R (>= 3.6.0)", + "zoo (>= 1.7-12)" + ], + "Imports": [ + "methods" + ], + "LinkingTo": [ + "zoo" + ], + "Suggests": [ + "timeSeries", + "timeDate", + "tseries", + "chron", + "tinytest" + ], + "LazyLoad": "yes", + "Description": "Provide for uniform handling of R's different time-based data classes by extending zoo, maximizing native format information preservation and allowing for user level customization and extension, while simplifying cross-class interoperability.", + "License": "GPL (>= 2)", + "URL": "https://joshuaulrich.github.io/xts/, https://github.com/joshuaulrich/xts", + "BugReports": "https://github.com/joshuaulrich/xts/issues", + "Encoding": "UTF-8", + "NeedsCompilation": "yes", + "Author": "Jeffrey A. Ryan [aut, cph], Joshua M. Ulrich [cre, aut], Ross Bennett [ctb], Corwin Joy [ctb]", + "Maintainer": "Joshua M. Ulrich <josh.m.ulrich@gmail.com>", + "Repository": "CRAN" + }, + "yaml": { + "Package": "yaml", + "Version": "2.3.10", + "Source": "Repository", + "Type": "Package", + "Title": "Methods to Convert R Data to YAML and Back", + "Date": "2024-07-22", + "Suggests": [ + "RUnit" + ], + "Author": "Shawn P Garbett [aut], Jeremy Stephens [aut, cre], Kirill Simonov [aut], Yihui Xie [ctb], Zhuoer Dong [ctb], Hadley Wickham [ctb], Jeffrey Horner [ctb], reikoch [ctb], Will Beasley [ctb], Brendan O'Connor [ctb], Gregory R. Warnes [ctb], Michael Quinn [ctb], Zhian N. Kamvar [ctb], Charlie Gao [ctb]", + "Maintainer": "Shawn Garbett <shawn.garbett@vumc.org>", + "License": "BSD_3_clause + file LICENSE", + "Description": "Implements the 'libyaml' 'YAML' 1.1 parser and emitter (<https://pyyaml.org/wiki/LibYAML>) for R.", + "URL": "https://github.com/vubiostat/r-yaml/", + "BugReports": "https://github.com/vubiostat/r-yaml/issues", + "NeedsCompilation": "yes", + "Repository": "CRAN" + }, + "zoo": { + "Package": "zoo", + "Version": "1.8-13", + "Source": "Repository", + "Date": "2025-02-20", + "Title": "S3 Infrastructure for Regular and Irregular Time Series (Z's Ordered Observations)", + "Authors@R": "c(person(given = \"Achim\", family = \"Zeileis\", role = c(\"aut\", \"cre\"), email = \"Achim.Zeileis@R-project.org\", comment = c(ORCID = \"0000-0003-0918-3766\")), person(given = \"Gabor\", family = \"Grothendieck\", role = \"aut\", email = \"ggrothendieck@gmail.com\"), person(given = c(\"Jeffrey\", \"A.\"), family = \"Ryan\", role = \"aut\", email = \"jeff.a.ryan@gmail.com\"), person(given = c(\"Joshua\", \"M.\"), family = \"Ulrich\", role = \"ctb\", email = \"josh.m.ulrich@gmail.com\"), person(given = \"Felix\", family = \"Andrews\", role = \"ctb\", email = \"felix@nfrac.org\"))", + "Description": "An S3 class with methods for totally ordered indexed observations. It is particularly aimed at irregular time series of numeric vectors/matrices and factors. zoo's key design goals are independence of a particular index/date/time class and consistency with ts and base R by providing methods to extend standard generics.", + "Depends": [ + "R (>= 3.1.0)", + "stats" + ], + "Suggests": [ + "AER", + "coda", + "chron", + "ggplot2 (>= 3.0.0)", + "mondate", + "scales", + "stinepack", + "strucchange", + "timeDate", + "timeSeries", + "tinyplot", + "tis", + "tseries", + "xts" + ], + "Imports": [ + "utils", + "graphics", + "grDevices", + "lattice (>= 0.20-27)" + ], + "License": "GPL-2 | GPL-3", + "URL": "https://zoo.R-Forge.R-project.org/", + "NeedsCompilation": "yes", + "Author": "Achim Zeileis [aut, cre] (<https://orcid.org/0000-0003-0918-3766>), Gabor Grothendieck [aut], Jeffrey A. Ryan [aut], Joshua M. Ulrich [ctb], Felix Andrews [ctb]", + "Maintainer": "Achim Zeileis <Achim.Zeileis@R-project.org>", + "Repository": "CRAN" + } + } +} diff --git a/renv/.gitignore b/renv/.gitignore new file mode 100644 index 0000000000000000000000000000000000000000..0ec0cbba2d7755cbd91956afaa585449906a1e16 --- /dev/null +++ b/renv/.gitignore @@ -0,0 +1,7 @@ +library/ +local/ +cellar/ +lock/ +python/ +sandbox/ +staging/ diff --git a/renv/activate.R b/renv/activate.R new file mode 100644 index 0000000000000000000000000000000000000000..2fe247d25264d6bb9e84ac8ef43db4f5978a415a --- /dev/null +++ b/renv/activate.R @@ -0,0 +1,1313 @@ + +local({ + + # the requested version of renv + version <- "1.1.1" + attr(version, "sha") <- NULL + + # the project directory + project <- Sys.getenv("RENV_PROJECT") + if (!nzchar(project)) + project <- getwd() + + # use start-up diagnostics if enabled + diagnostics <- Sys.getenv("RENV_STARTUP_DIAGNOSTICS", unset = "FALSE") + if (diagnostics) { + start <- Sys.time() + profile <- tempfile("renv-startup-", fileext = ".Rprof") + utils::Rprof(profile) + on.exit({ + utils::Rprof(NULL) + elapsed <- signif(difftime(Sys.time(), start, units = "auto"), digits = 2L) + writeLines(sprintf("- renv took %s to run the autoloader.", format(elapsed))) + writeLines(sprintf("- Profile: %s", profile)) + print(utils::summaryRprof(profile)) + }, add = TRUE) + } + + # figure out whether the autoloader is enabled + enabled <- local({ + + # first, check config option + override <- getOption("renv.config.autoloader.enabled") + if (!is.null(override)) + return(override) + + # if we're being run in a context where R_LIBS is already set, + # don't load -- presumably we're being run as a sub-process and + # the parent process has already set up library paths for us + rcmd <- Sys.getenv("R_CMD", unset = NA) + rlibs <- Sys.getenv("R_LIBS", unset = NA) + if (!is.na(rlibs) && !is.na(rcmd)) + return(FALSE) + + # next, check environment variables + # prefer using the configuration one in the future + envvars <- c( + "RENV_CONFIG_AUTOLOADER_ENABLED", + "RENV_AUTOLOADER_ENABLED", + "RENV_ACTIVATE_PROJECT" + ) + + for (envvar in envvars) { + envval <- Sys.getenv(envvar, unset = NA) + if (!is.na(envval)) + return(tolower(envval) %in% c("true", "t", "1")) + } + + # enable by default + TRUE + + }) + + # bail if we're not enabled + if (!enabled) { + + # if we're not enabled, we might still need to manually load + # the user profile here + profile <- Sys.getenv("R_PROFILE_USER", unset = "~/.Rprofile") + if (file.exists(profile)) { + cfg <- Sys.getenv("RENV_CONFIG_USER_PROFILE", unset = "TRUE") + if (tolower(cfg) %in% c("true", "t", "1")) + sys.source(profile, envir = globalenv()) + } + + return(FALSE) + + } + + # avoid recursion + if (identical(getOption("renv.autoloader.running"), TRUE)) { + warning("ignoring recursive attempt to run renv autoloader") + return(invisible(TRUE)) + } + + # signal that we're loading renv during R startup + options(renv.autoloader.running = TRUE) + on.exit(options(renv.autoloader.running = NULL), add = TRUE) + + # signal that we've consented to use renv + options(renv.consent = TRUE) + + # load the 'utils' package eagerly -- this ensures that renv shims, which + # mask 'utils' packages, will come first on the search path + library(utils, lib.loc = .Library) + + # unload renv if it's already been loaded + if ("renv" %in% loadedNamespaces()) + unloadNamespace("renv") + + # load bootstrap tools + ansify <- function(text) { + if (renv_ansify_enabled()) + renv_ansify_enhanced(text) + else + renv_ansify_default(text) + } + + renv_ansify_enabled <- function() { + + override <- Sys.getenv("RENV_ANSIFY_ENABLED", unset = NA) + if (!is.na(override)) + return(as.logical(override)) + + pane <- Sys.getenv("RSTUDIO_CHILD_PROCESS_PANE", unset = NA) + if (identical(pane, "build")) + return(FALSE) + + testthat <- Sys.getenv("TESTTHAT", unset = "false") + if (tolower(testthat) %in% "true") + return(FALSE) + + iderun <- Sys.getenv("R_CLI_HAS_HYPERLINK_IDE_RUN", unset = "false") + if (tolower(iderun) %in% "false") + return(FALSE) + + TRUE + + } + + renv_ansify_default <- function(text) { + text + } + + renv_ansify_enhanced <- function(text) { + + # R help links + pattern <- "`\\?(renv::(?:[^`])+)`" + replacement <- "`\033]8;;x-r-help:\\1\a?\\1\033]8;;\a`" + text <- gsub(pattern, replacement, text, perl = TRUE) + + # runnable code + pattern <- "`(renv::(?:[^`])+)`" + replacement <- "`\033]8;;x-r-run:\\1\a\\1\033]8;;\a`" + text <- gsub(pattern, replacement, text, perl = TRUE) + + # return ansified text + text + + } + + renv_ansify_init <- function() { + + envir <- renv_envir_self() + if (renv_ansify_enabled()) + assign("ansify", renv_ansify_enhanced, envir = envir) + else + assign("ansify", renv_ansify_default, envir = envir) + + } + + `%||%` <- function(x, y) { + if (is.null(x)) y else x + } + + catf <- function(fmt, ..., appendLF = TRUE) { + + quiet <- getOption("renv.bootstrap.quiet", default = FALSE) + if (quiet) + return(invisible()) + + msg <- sprintf(fmt, ...) + cat(msg, file = stdout(), sep = if (appendLF) "\n" else "") + + invisible(msg) + + } + + header <- function(label, + ..., + prefix = "#", + suffix = "-", + n = min(getOption("width"), 78)) + { + label <- sprintf(label, ...) + n <- max(n - nchar(label) - nchar(prefix) - 2L, 8L) + if (n <= 0) + return(paste(prefix, label)) + + tail <- paste(rep.int(suffix, n), collapse = "") + paste0(prefix, " ", label, " ", tail) + + } + + heredoc <- function(text, leave = 0) { + + # remove leading, trailing whitespace + trimmed <- gsub("^\\s*\\n|\\n\\s*$", "", text) + + # split into lines + lines <- strsplit(trimmed, "\n", fixed = TRUE)[[1L]] + + # compute common indent + indent <- regexpr("[^[:space:]]", lines) + common <- min(setdiff(indent, -1L)) - leave + text <- paste(substring(lines, common), collapse = "\n") + + # substitute in ANSI links for executable renv code + ansify(text) + + } + + bootstrap <- function(version, library) { + + friendly <- renv_bootstrap_version_friendly(version) + section <- header(sprintf("Bootstrapping renv %s", friendly)) + catf(section) + + # attempt to download renv + catf("- Downloading renv ... ", appendLF = FALSE) + withCallingHandlers( + tarball <- renv_bootstrap_download(version), + error = function(err) { + catf("FAILED") + stop("failed to download:\n", conditionMessage(err)) + } + ) + catf("OK") + on.exit(unlink(tarball), add = TRUE) + + # now attempt to install + catf("- Installing renv ... ", appendLF = FALSE) + withCallingHandlers( + status <- renv_bootstrap_install(version, tarball, library), + error = function(err) { + catf("FAILED") + stop("failed to install:\n", conditionMessage(err)) + } + ) + catf("OK") + + # add empty line to break up bootstrapping from normal output + catf("") + + return(invisible()) + } + + renv_bootstrap_tests_running <- function() { + getOption("renv.tests.running", default = FALSE) + } + + renv_bootstrap_repos <- function() { + + # get CRAN repository + cran <- getOption("renv.repos.cran", "https://cloud.r-project.org") + + # check for repos override + repos <- Sys.getenv("RENV_CONFIG_REPOS_OVERRIDE", unset = NA) + if (!is.na(repos)) { + + # check for RSPM; if set, use a fallback repository for renv + rspm <- Sys.getenv("RSPM", unset = NA) + if (identical(rspm, repos)) + repos <- c(RSPM = rspm, CRAN = cran) + + return(repos) + + } + + # check for lockfile repositories + repos <- tryCatch(renv_bootstrap_repos_lockfile(), error = identity) + if (!inherits(repos, "error") && length(repos)) + return(repos) + + # retrieve current repos + repos <- getOption("repos") + + # ensure @CRAN@ entries are resolved + repos[repos == "@CRAN@"] <- cran + + # add in renv.bootstrap.repos if set + default <- c(FALLBACK = "https://cloud.r-project.org") + extra <- getOption("renv.bootstrap.repos", default = default) + repos <- c(repos, extra) + + # remove duplicates that might've snuck in + dupes <- duplicated(repos) | duplicated(names(repos)) + repos[!dupes] + + } + + renv_bootstrap_repos_lockfile <- function() { + + lockpath <- Sys.getenv("RENV_PATHS_LOCKFILE", unset = "renv.lock") + if (!file.exists(lockpath)) + return(NULL) + + lockfile <- tryCatch(renv_json_read(lockpath), error = identity) + if (inherits(lockfile, "error")) { + warning(lockfile) + return(NULL) + } + + repos <- lockfile$R$Repositories + if (length(repos) == 0) + return(NULL) + + keys <- vapply(repos, `[[`, "Name", FUN.VALUE = character(1)) + vals <- vapply(repos, `[[`, "URL", FUN.VALUE = character(1)) + names(vals) <- keys + + return(vals) + + } + + renv_bootstrap_download <- function(version) { + + sha <- attr(version, "sha", exact = TRUE) + + methods <- if (!is.null(sha)) { + + # attempting to bootstrap a development version of renv + c( + function() renv_bootstrap_download_tarball(sha), + function() renv_bootstrap_download_github(sha) + ) + + } else { + + # attempting to bootstrap a release version of renv + c( + function() renv_bootstrap_download_tarball(version), + function() renv_bootstrap_download_cran_latest(version), + function() renv_bootstrap_download_cran_archive(version) + ) + + } + + for (method in methods) { + path <- tryCatch(method(), error = identity) + if (is.character(path) && file.exists(path)) + return(path) + } + + stop("All download methods failed") + + } + + renv_bootstrap_download_impl <- function(url, destfile) { + + mode <- "wb" + + # https://bugs.r-project.org/bugzilla/show_bug.cgi?id=17715 + fixup <- + Sys.info()[["sysname"]] == "Windows" && + substring(url, 1L, 5L) == "file:" + + if (fixup) + mode <- "w+b" + + args <- list( + url = url, + destfile = destfile, + mode = mode, + quiet = TRUE + ) + + if ("headers" %in% names(formals(utils::download.file))) { + headers <- renv_bootstrap_download_custom_headers(url) + if (length(headers) && is.character(headers)) + args$headers <- headers + } + + do.call(utils::download.file, args) + + } + + renv_bootstrap_download_custom_headers <- function(url) { + + headers <- getOption("renv.download.headers") + if (is.null(headers)) + return(character()) + + if (!is.function(headers)) + stopf("'renv.download.headers' is not a function") + + headers <- headers(url) + if (length(headers) == 0L) + return(character()) + + if (is.list(headers)) + headers <- unlist(headers, recursive = FALSE, use.names = TRUE) + + ok <- + is.character(headers) && + is.character(names(headers)) && + all(nzchar(names(headers))) + + if (!ok) + stop("invocation of 'renv.download.headers' did not return a named character vector") + + headers + + } + + renv_bootstrap_download_cran_latest <- function(version) { + + spec <- renv_bootstrap_download_cran_latest_find(version) + type <- spec$type + repos <- spec$repos + + baseurl <- utils::contrib.url(repos = repos, type = type) + ext <- if (identical(type, "source")) + ".tar.gz" + else if (Sys.info()[["sysname"]] == "Windows") + ".zip" + else + ".tgz" + name <- sprintf("renv_%s%s", version, ext) + url <- paste(baseurl, name, sep = "/") + + destfile <- file.path(tempdir(), name) + status <- tryCatch( + renv_bootstrap_download_impl(url, destfile), + condition = identity + ) + + if (inherits(status, "condition")) + return(FALSE) + + # report success and return + destfile + + } + + renv_bootstrap_download_cran_latest_find <- function(version) { + + # check whether binaries are supported on this system + binary <- + getOption("renv.bootstrap.binary", default = TRUE) && + !identical(.Platform$pkgType, "source") && + !identical(getOption("pkgType"), "source") && + Sys.info()[["sysname"]] %in% c("Darwin", "Windows") + + types <- c(if (binary) "binary", "source") + + # iterate over types + repositories + for (type in types) { + for (repos in renv_bootstrap_repos()) { + + # build arguments for utils::available.packages() call + args <- list(type = type, repos = repos) + + # add custom headers if available -- note that + # utils::available.packages() will pass this to download.file() + if ("headers" %in% names(formals(utils::download.file))) { + headers <- renv_bootstrap_download_custom_headers(repos) + if (length(headers) && is.character(headers)) + args$headers <- headers + } + + # retrieve package database + db <- tryCatch( + as.data.frame( + do.call(utils::available.packages, args), + stringsAsFactors = FALSE + ), + error = identity + ) + + if (inherits(db, "error")) + next + + # check for compatible entry + entry <- db[db$Package %in% "renv" & db$Version %in% version, ] + if (nrow(entry) == 0) + next + + # found it; return spec to caller + spec <- list(entry = entry, type = type, repos = repos) + return(spec) + + } + } + + # if we got here, we failed to find renv + fmt <- "renv %s is not available from your declared package repositories" + stop(sprintf(fmt, version)) + + } + + renv_bootstrap_download_cran_archive <- function(version) { + + name <- sprintf("renv_%s.tar.gz", version) + repos <- renv_bootstrap_repos() + urls <- file.path(repos, "src/contrib/Archive/renv", name) + destfile <- file.path(tempdir(), name) + + for (url in urls) { + + status <- tryCatch( + renv_bootstrap_download_impl(url, destfile), + condition = identity + ) + + if (identical(status, 0L)) + return(destfile) + + } + + return(FALSE) + + } + + renv_bootstrap_download_tarball <- function(version) { + + # if the user has provided the path to a tarball via + # an environment variable, then use it + tarball <- Sys.getenv("RENV_BOOTSTRAP_TARBALL", unset = NA) + if (is.na(tarball)) + return() + + # allow directories + if (dir.exists(tarball)) { + name <- sprintf("renv_%s.tar.gz", version) + tarball <- file.path(tarball, name) + } + + # bail if it doesn't exist + if (!file.exists(tarball)) { + + # let the user know we weren't able to honour their request + fmt <- "- RENV_BOOTSTRAP_TARBALL is set (%s) but does not exist." + msg <- sprintf(fmt, tarball) + warning(msg) + + # bail + return() + + } + + catf("- Using local tarball '%s'.", tarball) + tarball + + } + + renv_bootstrap_github_token <- function() { + for (envvar in c("GITHUB_TOKEN", "GITHUB_PAT", "GH_TOKEN")) { + envval <- Sys.getenv(envvar, unset = NA) + if (!is.na(envval)) + return(envval) + } + } + + renv_bootstrap_download_github <- function(version) { + + enabled <- Sys.getenv("RENV_BOOTSTRAP_FROM_GITHUB", unset = "TRUE") + if (!identical(enabled, "TRUE")) + return(FALSE) + + # prepare download options + token <- renv_bootstrap_github_token() + if (is.null(token)) + token <- "" + + if (nzchar(Sys.which("curl")) && nzchar(token)) { + fmt <- "--location --fail --header \"Authorization: token %s\"" + extra <- sprintf(fmt, token) + saved <- options("download.file.method", "download.file.extra") + options(download.file.method = "curl", download.file.extra = extra) + on.exit(do.call(base::options, saved), add = TRUE) + } else if (nzchar(Sys.which("wget")) && nzchar(token)) { + fmt <- "--header=\"Authorization: token %s\"" + extra <- sprintf(fmt, token) + saved <- options("download.file.method", "download.file.extra") + options(download.file.method = "wget", download.file.extra = extra) + on.exit(do.call(base::options, saved), add = TRUE) + } + + url <- file.path("https://api.github.com/repos/rstudio/renv/tarball", version) + name <- sprintf("renv_%s.tar.gz", version) + destfile <- file.path(tempdir(), name) + + status <- tryCatch( + renv_bootstrap_download_impl(url, destfile), + condition = identity + ) + + if (!identical(status, 0L)) + return(FALSE) + + renv_bootstrap_download_augment(destfile) + + return(destfile) + + } + + # Add Sha to DESCRIPTION. This is stop gap until #890, after which we + # can use renv::install() to fully capture metadata. + renv_bootstrap_download_augment <- function(destfile) { + sha <- renv_bootstrap_git_extract_sha1_tar(destfile) + if (is.null(sha)) { + return() + } + + # Untar + tempdir <- tempfile("renv-github-") + on.exit(unlink(tempdir, recursive = TRUE), add = TRUE) + untar(destfile, exdir = tempdir) + pkgdir <- dir(tempdir, full.names = TRUE)[[1]] + + # Modify description + desc_path <- file.path(pkgdir, "DESCRIPTION") + desc_lines <- readLines(desc_path) + remotes_fields <- c( + "RemoteType: github", + "RemoteHost: api.github.com", + "RemoteRepo: renv", + "RemoteUsername: rstudio", + "RemotePkgRef: rstudio/renv", + paste("RemoteRef: ", sha), + paste("RemoteSha: ", sha) + ) + writeLines(c(desc_lines[desc_lines != ""], remotes_fields), con = desc_path) + + # Re-tar + local({ + old <- setwd(tempdir) + on.exit(setwd(old), add = TRUE) + + tar(destfile, compression = "gzip") + }) + invisible() + } + + # Extract the commit hash from a git archive. Git archives include the SHA1 + # hash as the comment field of the tarball pax extended header + # (see https://www.kernel.org/pub/software/scm/git/docs/git-archive.html) + # For GitHub archives this should be the first header after the default one + # (512 byte) header. + renv_bootstrap_git_extract_sha1_tar <- function(bundle) { + + # open the bundle for reading + # We use gzcon for everything because (from ?gzcon) + # > Reading from a connection which does not supply a 'gzip' magic + # > header is equivalent to reading from the original connection + conn <- gzcon(file(bundle, open = "rb", raw = TRUE)) + on.exit(close(conn)) + + # The default pax header is 512 bytes long and the first pax extended header + # with the comment should be 51 bytes long + # `52 comment=` (11 chars) + 40 byte SHA1 hash + len <- 0x200 + 0x33 + res <- rawToChar(readBin(conn, "raw", n = len)[0x201:len]) + + if (grepl("^52 comment=", res)) { + sub("52 comment=", "", res) + } else { + NULL + } + } + + renv_bootstrap_install <- function(version, tarball, library) { + + # attempt to install it into project library + dir.create(library, showWarnings = FALSE, recursive = TRUE) + output <- renv_bootstrap_install_impl(library, tarball) + + # check for successful install + status <- attr(output, "status") + if (is.null(status) || identical(status, 0L)) + return(status) + + # an error occurred; report it + header <- "installation of renv failed" + lines <- paste(rep.int("=", nchar(header)), collapse = "") + text <- paste(c(header, lines, output), collapse = "\n") + stop(text) + + } + + renv_bootstrap_install_impl <- function(library, tarball) { + + # invoke using system2 so we can capture and report output + bin <- R.home("bin") + exe <- if (Sys.info()[["sysname"]] == "Windows") "R.exe" else "R" + R <- file.path(bin, exe) + + args <- c( + "--vanilla", "CMD", "INSTALL", "--no-multiarch", + "-l", shQuote(path.expand(library)), + shQuote(path.expand(tarball)) + ) + + system2(R, args, stdout = TRUE, stderr = TRUE) + + } + + renv_bootstrap_platform_prefix <- function() { + + # construct version prefix + version <- paste(R.version$major, R.version$minor, sep = ".") + prefix <- paste("R", numeric_version(version)[1, 1:2], sep = "-") + + # include SVN revision for development versions of R + # (to avoid sharing platform-specific artefacts with released versions of R) + devel <- + identical(R.version[["status"]], "Under development (unstable)") || + identical(R.version[["nickname"]], "Unsuffered Consequences") + + if (devel) + prefix <- paste(prefix, R.version[["svn rev"]], sep = "-r") + + # build list of path components + components <- c(prefix, R.version$platform) + + # include prefix if provided by user + prefix <- renv_bootstrap_platform_prefix_impl() + if (!is.na(prefix) && nzchar(prefix)) + components <- c(prefix, components) + + # build prefix + paste(components, collapse = "/") + + } + + renv_bootstrap_platform_prefix_impl <- function() { + + # if an explicit prefix has been supplied, use it + prefix <- Sys.getenv("RENV_PATHS_PREFIX", unset = NA) + if (!is.na(prefix)) + return(prefix) + + # if the user has requested an automatic prefix, generate it + auto <- Sys.getenv("RENV_PATHS_PREFIX_AUTO", unset = NA) + if (is.na(auto) && getRversion() >= "4.4.0") + auto <- "TRUE" + + if (auto %in% c("TRUE", "True", "true", "1")) + return(renv_bootstrap_platform_prefix_auto()) + + # empty string on failure + "" + + } + + renv_bootstrap_platform_prefix_auto <- function() { + + prefix <- tryCatch(renv_bootstrap_platform_os(), error = identity) + if (inherits(prefix, "error") || prefix %in% "unknown") { + + msg <- paste( + "failed to infer current operating system", + "please file a bug report at https://github.com/rstudio/renv/issues", + sep = "; " + ) + + warning(msg) + + } + + prefix + + } + + renv_bootstrap_platform_os <- function() { + + sysinfo <- Sys.info() + sysname <- sysinfo[["sysname"]] + + # handle Windows + macOS up front + if (sysname == "Windows") + return("windows") + else if (sysname == "Darwin") + return("macos") + + # check for os-release files + for (file in c("/etc/os-release", "/usr/lib/os-release")) + if (file.exists(file)) + return(renv_bootstrap_platform_os_via_os_release(file, sysinfo)) + + # check for redhat-release files + if (file.exists("/etc/redhat-release")) + return(renv_bootstrap_platform_os_via_redhat_release()) + + "unknown" + + } + + renv_bootstrap_platform_os_via_os_release <- function(file, sysinfo) { + + # read /etc/os-release + release <- utils::read.table( + file = file, + sep = "=", + quote = c("\"", "'"), + col.names = c("Key", "Value"), + comment.char = "#", + stringsAsFactors = FALSE + ) + + vars <- as.list(release$Value) + names(vars) <- release$Key + + # get os name + os <- tolower(sysinfo[["sysname"]]) + + # read id + id <- "unknown" + for (field in c("ID", "ID_LIKE")) { + if (field %in% names(vars) && nzchar(vars[[field]])) { + id <- vars[[field]] + break + } + } + + # read version + version <- "unknown" + for (field in c("UBUNTU_CODENAME", "VERSION_CODENAME", "VERSION_ID", "BUILD_ID")) { + if (field %in% names(vars) && nzchar(vars[[field]])) { + version <- vars[[field]] + break + } + } + + # join together + paste(c(os, id, version), collapse = "-") + + } + + renv_bootstrap_platform_os_via_redhat_release <- function() { + + # read /etc/redhat-release + contents <- readLines("/etc/redhat-release", warn = FALSE) + + # infer id + id <- if (grepl("centos", contents, ignore.case = TRUE)) + "centos" + else if (grepl("redhat", contents, ignore.case = TRUE)) + "redhat" + else + "unknown" + + # try to find a version component (very hacky) + version <- "unknown" + + parts <- strsplit(contents, "[[:space:]]")[[1L]] + for (part in parts) { + + nv <- tryCatch(numeric_version(part), error = identity) + if (inherits(nv, "error")) + next + + version <- nv[1, 1] + break + + } + + paste(c("linux", id, version), collapse = "-") + + } + + renv_bootstrap_library_root_name <- function(project) { + + # use project name as-is if requested + asis <- Sys.getenv("RENV_PATHS_LIBRARY_ROOT_ASIS", unset = "FALSE") + if (asis) + return(basename(project)) + + # otherwise, disambiguate based on project's path + id <- substring(renv_bootstrap_hash_text(project), 1L, 8L) + paste(basename(project), id, sep = "-") + + } + + renv_bootstrap_library_root <- function(project) { + + prefix <- renv_bootstrap_profile_prefix() + + path <- Sys.getenv("RENV_PATHS_LIBRARY", unset = NA) + if (!is.na(path)) + return(paste(c(path, prefix), collapse = "/")) + + path <- renv_bootstrap_library_root_impl(project) + if (!is.null(path)) { + name <- renv_bootstrap_library_root_name(project) + return(paste(c(path, prefix, name), collapse = "/")) + } + + renv_bootstrap_paths_renv("library", project = project) + + } + + renv_bootstrap_library_root_impl <- function(project) { + + root <- Sys.getenv("RENV_PATHS_LIBRARY_ROOT", unset = NA) + if (!is.na(root)) + return(root) + + type <- renv_bootstrap_project_type(project) + if (identical(type, "package")) { + userdir <- renv_bootstrap_user_dir() + return(file.path(userdir, "library")) + } + + } + + renv_bootstrap_validate_version <- function(version, description = NULL) { + + # resolve description file + # + # avoid passing lib.loc to `packageDescription()` below, since R will + # use the loaded version of the package by default anyhow. note that + # this function should only be called after 'renv' is loaded + # https://github.com/rstudio/renv/issues/1625 + description <- description %||% packageDescription("renv") + + # check whether requested version 'version' matches loaded version of renv + sha <- attr(version, "sha", exact = TRUE) + valid <- if (!is.null(sha)) + renv_bootstrap_validate_version_dev(sha, description) + else + renv_bootstrap_validate_version_release(version, description) + + if (valid) + return(TRUE) + + # the loaded version of renv doesn't match the requested version; + # give the user instructions on how to proceed + dev <- identical(description[["RemoteType"]], "github") + remote <- if (dev) + paste("rstudio/renv", description[["RemoteSha"]], sep = "@") + else + paste("renv", description[["Version"]], sep = "@") + + # display both loaded version + sha if available + friendly <- renv_bootstrap_version_friendly( + version = description[["Version"]], + sha = if (dev) description[["RemoteSha"]] + ) + + fmt <- heredoc(" + renv %1$s was loaded from project library, but this project is configured to use renv %2$s. + - Use `renv::record(\"%3$s\")` to record renv %1$s in the lockfile. + - Use `renv::restore(packages = \"renv\")` to install renv %2$s into the project library. + ") + catf(fmt, friendly, renv_bootstrap_version_friendly(version), remote) + + FALSE + + } + + renv_bootstrap_validate_version_dev <- function(version, description) { + + expected <- description[["RemoteSha"]] + if (!is.character(expected)) + return(FALSE) + + pattern <- sprintf("^\\Q%s\\E", version) + grepl(pattern, expected, perl = TRUE) + + } + + renv_bootstrap_validate_version_release <- function(version, description) { + expected <- description[["Version"]] + is.character(expected) && identical(expected, version) + } + + renv_bootstrap_hash_text <- function(text) { + + hashfile <- tempfile("renv-hash-") + on.exit(unlink(hashfile), add = TRUE) + + writeLines(text, con = hashfile) + tools::md5sum(hashfile) + + } + + renv_bootstrap_load <- function(project, libpath, version) { + + # try to load renv from the project library + if (!requireNamespace("renv", lib.loc = libpath, quietly = TRUE)) + return(FALSE) + + # warn if the version of renv loaded does not match + renv_bootstrap_validate_version(version) + + # execute renv load hooks, if any + hooks <- getHook("renv::autoload") + for (hook in hooks) + if (is.function(hook)) + tryCatch(hook(), error = warnify) + + # load the project + renv::load(project) + + TRUE + + } + + renv_bootstrap_profile_load <- function(project) { + + # if RENV_PROFILE is already set, just use that + profile <- Sys.getenv("RENV_PROFILE", unset = NA) + if (!is.na(profile) && nzchar(profile)) + return(profile) + + # check for a profile file (nothing to do if it doesn't exist) + path <- renv_bootstrap_paths_renv("profile", profile = FALSE, project = project) + if (!file.exists(path)) + return(NULL) + + # read the profile, and set it if it exists + contents <- readLines(path, warn = FALSE) + if (length(contents) == 0L) + return(NULL) + + # set RENV_PROFILE + profile <- contents[[1L]] + if (!profile %in% c("", "default")) + Sys.setenv(RENV_PROFILE = profile) + + profile + + } + + renv_bootstrap_profile_prefix <- function() { + profile <- renv_bootstrap_profile_get() + if (!is.null(profile)) + return(file.path("profiles", profile, "renv")) + } + + renv_bootstrap_profile_get <- function() { + profile <- Sys.getenv("RENV_PROFILE", unset = "") + renv_bootstrap_profile_normalize(profile) + } + + renv_bootstrap_profile_set <- function(profile) { + profile <- renv_bootstrap_profile_normalize(profile) + if (is.null(profile)) + Sys.unsetenv("RENV_PROFILE") + else + Sys.setenv(RENV_PROFILE = profile) + } + + renv_bootstrap_profile_normalize <- function(profile) { + + if (is.null(profile) || profile %in% c("", "default")) + return(NULL) + + profile + + } + + renv_bootstrap_path_absolute <- function(path) { + + substr(path, 1L, 1L) %in% c("~", "/", "\\") || ( + substr(path, 1L, 1L) %in% c(letters, LETTERS) && + substr(path, 2L, 3L) %in% c(":/", ":\\") + ) + + } + + renv_bootstrap_paths_renv <- function(..., profile = TRUE, project = NULL) { + renv <- Sys.getenv("RENV_PATHS_RENV", unset = "renv") + root <- if (renv_bootstrap_path_absolute(renv)) NULL else project + prefix <- if (profile) renv_bootstrap_profile_prefix() + components <- c(root, renv, prefix, ...) + paste(components, collapse = "/") + } + + renv_bootstrap_project_type <- function(path) { + + descpath <- file.path(path, "DESCRIPTION") + if (!file.exists(descpath)) + return("unknown") + + desc <- tryCatch( + read.dcf(descpath, all = TRUE), + error = identity + ) + + if (inherits(desc, "error")) + return("unknown") + + type <- desc$Type + if (!is.null(type)) + return(tolower(type)) + + package <- desc$Package + if (!is.null(package)) + return("package") + + "unknown" + + } + + renv_bootstrap_user_dir <- function() { + dir <- renv_bootstrap_user_dir_impl() + path.expand(chartr("\\", "/", dir)) + } + + renv_bootstrap_user_dir_impl <- function() { + + # use local override if set + override <- getOption("renv.userdir.override") + if (!is.null(override)) + return(override) + + # use R_user_dir if available + tools <- asNamespace("tools") + if (is.function(tools$R_user_dir)) + return(tools$R_user_dir("renv", "cache")) + + # try using our own backfill for older versions of R + envvars <- c("R_USER_CACHE_DIR", "XDG_CACHE_HOME") + for (envvar in envvars) { + root <- Sys.getenv(envvar, unset = NA) + if (!is.na(root)) + return(file.path(root, "R/renv")) + } + + # use platform-specific default fallbacks + if (Sys.info()[["sysname"]] == "Windows") + file.path(Sys.getenv("LOCALAPPDATA"), "R/cache/R/renv") + else if (Sys.info()[["sysname"]] == "Darwin") + "~/Library/Caches/org.R-project.R/R/renv" + else + "~/.cache/R/renv" + + } + + renv_bootstrap_version_friendly <- function(version, shafmt = NULL, sha = NULL) { + sha <- sha %||% attr(version, "sha", exact = TRUE) + parts <- c(version, sprintf(shafmt %||% " [sha: %s]", substring(sha, 1L, 7L))) + paste(parts, collapse = "") + } + + renv_bootstrap_exec <- function(project, libpath, version) { + if (!renv_bootstrap_load(project, libpath, version)) + renv_bootstrap_run(project, libpath, version) + } + + renv_bootstrap_run <- function(project, libpath, version) { + + # perform bootstrap + bootstrap(version, libpath) + + # exit early if we're just testing bootstrap + if (!is.na(Sys.getenv("RENV_BOOTSTRAP_INSTALL_ONLY", unset = NA))) + return(TRUE) + + # try again to load + if (requireNamespace("renv", lib.loc = libpath, quietly = TRUE)) { + return(renv::load(project = project)) + } + + # failed to download or load renv; warn the user + msg <- c( + "Failed to find an renv installation: the project will not be loaded.", + "Use `renv::activate()` to re-initialize the project." + ) + + warning(paste(msg, collapse = "\n"), call. = FALSE) + + } + + renv_json_read <- function(file = NULL, text = NULL) { + + jlerr <- NULL + + # if jsonlite is loaded, use that instead + if ("jsonlite" %in% loadedNamespaces()) { + + json <- tryCatch(renv_json_read_jsonlite(file, text), error = identity) + if (!inherits(json, "error")) + return(json) + + jlerr <- json + + } + + # otherwise, fall back to the default JSON reader + json <- tryCatch(renv_json_read_default(file, text), error = identity) + if (!inherits(json, "error")) + return(json) + + # report an error + if (!is.null(jlerr)) + stop(jlerr) + else + stop(json) + + } + + renv_json_read_jsonlite <- function(file = NULL, text = NULL) { + text <- paste(text %||% readLines(file, warn = FALSE), collapse = "\n") + jsonlite::fromJSON(txt = text, simplifyVector = FALSE) + } + + renv_json_read_patterns <- function() { + + list( + + # objects + list("{", "\t\n\tobject(\t\n\t"), + list("}", "\t\n\t)\t\n\t"), + + # arrays + list("[", "\t\n\tarray(\t\n\t"), + list("]", "\n\t\n)\n\t\n"), + + # maps + list(":", "\t\n\t=\t\n\t") + + ) + + } + + renv_json_read_envir <- function() { + + envir <- new.env(parent = emptyenv()) + + envir[["+"]] <- `+` + envir[["-"]] <- `-` + + envir[["object"]] <- function(...) { + result <- list(...) + names(result) <- as.character(names(result)) + result + } + + envir[["array"]] <- list + + envir[["true"]] <- TRUE + envir[["false"]] <- FALSE + envir[["null"]] <- NULL + + envir + + } + + renv_json_read_remap <- function(object, patterns) { + + # repair names if necessary + if (!is.null(names(object))) { + + nms <- names(object) + for (pattern in patterns) + nms <- gsub(pattern[[2L]], pattern[[1L]], nms, fixed = TRUE) + names(object) <- nms + + } + + # repair strings if necessary + if (is.character(object)) { + for (pattern in patterns) + object <- gsub(pattern[[2L]], pattern[[1L]], object, fixed = TRUE) + } + + # recurse for other objects + if (is.recursive(object)) + for (i in seq_along(object)) + object[i] <- list(renv_json_read_remap(object[[i]], patterns)) + + # return remapped object + object + + } + + renv_json_read_default <- function(file = NULL, text = NULL) { + + # read json text + text <- paste(text %||% readLines(file, warn = FALSE), collapse = "\n") + + # convert into something the R parser will understand + patterns <- renv_json_read_patterns() + transformed <- text + for (pattern in patterns) + transformed <- gsub(pattern[[1L]], pattern[[2L]], transformed, fixed = TRUE) + + # parse it + rfile <- tempfile("renv-json-", fileext = ".R") + on.exit(unlink(rfile), add = TRUE) + writeLines(transformed, con = rfile) + json <- parse(rfile, keep.source = FALSE, srcfile = NULL)[[1L]] + + # evaluate in safe environment + result <- eval(json, envir = renv_json_read_envir()) + + # fix up strings if necessary + renv_json_read_remap(result, patterns) + + } + + + # load the renv profile, if any + renv_bootstrap_profile_load(project) + + # construct path to library root + root <- renv_bootstrap_library_root(project) + + # construct library prefix for platform + prefix <- renv_bootstrap_platform_prefix() + + # construct full libpath + libpath <- file.path(root, prefix) + + # run bootstrap code + renv_bootstrap_exec(project, libpath, version) + + invisible() + +}) diff --git a/renv/settings.json b/renv/settings.json new file mode 100644 index 0000000000000000000000000000000000000000..74c1d4bb846f81c54728052b3d1f4b7f738e93c1 --- /dev/null +++ b/renv/settings.json @@ -0,0 +1,19 @@ +{ + "bioconductor.version": null, + "external.libraries": [], + "ignored.packages": [], + "package.dependency.fields": [ + "Imports", + "Depends", + "LinkingTo" + ], + "ppm.enabled": null, + "ppm.ignored.urls": [], + "r.version": null, + "snapshot.type": "explicit", + "use.cache": true, + "vcs.ignore.cellar": true, + "vcs.ignore.library": true, + "vcs.ignore.local": true, + "vcs.manage.ignores": true +}