diff --git a/.Rbuildignore b/.Rbuildignore index 95e6b03b..d752d52f 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -4,3 +4,5 @@ ^.venv ^schematic$ ^\.github$ +^.*\.Rproj$ +^\.Rproj\.user$ diff --git a/.Rprofile b/.Rprofile index 974262f3..f99102e0 100644 --- a/.Rprofile +++ b/.Rprofile @@ -2,8 +2,8 @@ source("renv/activate.R") .First <- function() { options( repos = c( - CRAN = "https://cran.rstudio.com/", - Sage = "http://ran.synapse.org" + binaries = "https://packagemanager.posit.co/cran/__linux__/noble/latest", + CRAN = "https://cran.rstudio.com/" ), sass.cache = FALSE, # turn of styling caching stringsAsFactors = FALSE # no needed if R >= 4.0.0 diff --git a/Dockerfile b/Dockerfile index d025a7bd..e5190530 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,4 +1,4 @@ -FROM ghcr.io/afwillia/shiny-base:release-1.12 +FROM ghcr.io/afwillia/shiny-base:release-1.13 # add version tag as a build argument ARG DCA_VERSION @@ -7,7 +7,7 @@ ENV DCA_VERSION=$DCA_VERSION USER root RUN apt-get update -RUN apt-get install -y libxml2 libglpk-dev libicu-dev libicu70 curl +RUN apt-get install -y libxml2 libglpk-dev libicu-dev curl # overwrite the default config with our modified copy COPY shiny-server.conf /etc/shiny-server/shiny-server.conf @@ -20,6 +20,6 @@ COPY --chown=shiny ./ ./ # set up r packages via renv. Use binary lib matching the shiny-base ubuntu version # to speed up installatioon. -RUN Rscript -e 'renv::restore(repos="https://packagemanager.rstudio.com/all/__linux__/jammy/latest"); renv::install("./")' +RUN Rscript -e 'renv::restore(repos="https://packagemanager.posit.co/cran/__linux__/noble/latest"); renv::install("./")' CMD ["./dca_startup.sh"] diff --git a/Shiny_App.Rproj b/Shiny_App.Rproj index 8e3c2ebc..21a4da08 100644 --- a/Shiny_App.Rproj +++ b/Shiny_App.Rproj @@ -11,3 +11,7 @@ Encoding: UTF-8 RnwWeave: Sweave LaTeX: pdfLaTeX + +BuildType: Package +PackageUseDevtools: Yes +PackageInstallArgs: --no-multiarch --with-keep.source diff --git a/renv.lock b/renv.lock index 0ea6f44b..e4739b7b 100644 --- a/renv.lock +++ b/renv.lock @@ -1,45 +1,65 @@ { "R": { - "Version": "4.1.3", + "Version": "4.4.1", "Repositories": [ { "Name": "CRAN", "URL": "https://cran.rstudio.com" }, { - "Name": "Sage", - "URL": "http://ran.synapse.org" - }, - { - "Name": "Rstudio-binaries", - "URL": "https://packagemanager.rstudio.com/all/__linux__/focal/latest" + "Name": "binaries", + "URL": "https://packagemanager.posit.co/cran/__linux__/noble/latest" } ] }, "Packages": { + "AsioHeaders": { + "Package": "AsioHeaders", + "Version": "1.22.1-2", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "85bf3bd8fa58da21a22d84fd4f4ef0a8" + }, "DT": { "Package": "DT", - "Version": "0.27", + "Version": "0.33", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "crosstalk", "htmltools", "htmlwidgets", + "httpuv", "jquerylib", "jsonlite", "magrittr", "promises" ], - "Hash": "3444e6ed78763f9f13aaa39f2481eb34" + "Hash": "64ff3427f559ce3f2597a4fe13255cb6" + }, + "MASS": { + "Package": "MASS", + "Version": "7.3-61", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "R", + "grDevices", + "graphics", + "methods", + "stats", + "utils" + ], + "Hash": "0cafd6f0500e5deba33be22c46bf6055" }, "Matrix": { "Package": "Matrix", - "Version": "1.5-3", + "Version": "1.7-1", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R", + "grDevices", "graphics", "grid", "lattice", @@ -47,7 +67,7 @@ "stats", "utils" ], - "Hash": "4006dffe49958d2dd591c17e61e60591" + "Hash": "5122bb14d8736372411f955e1b16bc8a" }, "R6": { "Package": "R6", @@ -59,16 +79,26 @@ ], "Hash": "470851b6d5d0ac559e9d01bb352b4021" }, + "RColorBrewer": { + "Package": "RColorBrewer", + "Version": "1.1-3", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "R" + ], + "Hash": "45f0398006e83a5b10b72a90663d8d8c" + }, "Rcpp": { "Package": "Rcpp", - "Version": "1.0.10", + "Version": "1.0.13", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "methods", "utils" ], - "Hash": "e749cae40fa9ef469b6050959517453c" + "Hash": "f27411eb6d9c3dada5edd444b8416675" }, "RcppTOML": { "Package": "RcppTOML", @@ -83,13 +113,13 @@ }, "askpass": { "Package": "askpass", - "Version": "1.1", + "Version": "1.2.1", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "sys" ], - "Hash": "e8a22846fff485f0be3770c2da758713" + "Hash": "c39f4155b3ceb1a9a2799d700fbd4b6a" }, "base64enc": { "Package": "base64enc", @@ -103,17 +133,17 @@ }, "bit": { "Package": "bit", - "Version": "4.0.5", + "Version": "4.5.0", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R" ], - "Hash": "d242abec29412ce988848d0294b208fd" + "Hash": "5dc7b2677d65d0e874fc4aaf0e879987" }, "bit64": { "Package": "bit64", - "Version": "4.0.5", + "Version": "4.5.2", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -123,49 +153,54 @@ "stats", "utils" ], - 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"crayon", - "digest", - "httr", - "jsonlite", + "grDevices", + "graphics", "methods", - "rex", - "stats", - "utils", - "withr", - "yaml" + "stats" ], - "Hash": "a861cee34fbb4b107a73dd414ef56724" + "Hash": "d954cb1c57e8d8b756165d7ba18aa55a" + }, + "commonmark": { + "Package": "commonmark", + "Version": "1.9.2", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "14eb0596f987c71535d07c3aff814742" }, "cpp11": { "Package": "cpp11", - "Version": "0.4.3", + "Version": "0.5.0", "Source": "Repository", "Repository": "CRAN", - "Hash": "ed588261931ee3be2c700d22e94a29ab" + "Requirements": [ + "R" + ], + "Hash": "91570bba75d0c9d3f1040c835cee8fba" }, "crayon": { "Package": "crayon", - "Version": "1.5.2", + "Version": "1.5.3", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -241,11 +283,11 @@ "methods", "utils" ], - "Hash": "e8a1e41acf02548751f45c718d55aa6a" + "Hash": "859d96e65ef198fd43e82b9628d593ef" }, "crosstalk": { "Package": "crosstalk", - "Version": "1.2.0", + "Version": "1.2.1", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -254,32 +296,32 @@ "jsonlite", "lazyeval" ], - 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"Version": "0.2.0", + "Version": "0.2.1", "Source": "Repository", "Repository": "CRAN", "Requirements": [ + "bslib", "htmltools", "rstudioapi", "sass", "shiny" ], - "Hash": "fa54367040deb4537da49b7ac0ee5770" + "Hash": "7bdb5c90d4fe3cb14dcefbe837ce01da" }, "fs": { "Package": "fs", - "Version": "1.6.1", + "Version": "1.6.4", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R", "methods" ], - "Hash": "f4dcd23b67e33d851d2079f703e8b985" + "Hash": "15aeb8c27f5ea5161f9f6a641fafd93a" }, "future": { "Package": "future", - "Version": "1.32.0", - "Source": "Repository" + "Version": "1.34.0", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "digest", + "globals", + "listenv", + "parallel", + "parallelly", + "utils" + ], + "Hash": "475771e3edb711591476be387c9a8c2e" }, "generics": { "Package": "generics", @@ -446,16 +493,68 @@ ], "Hash": "15e9634c0fcd294799e9b2e929ed1b86" }, + "ggplot2": { + "Package": "ggplot2", + "Version": "3.5.1", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "MASS", + "R", + "cli", + "glue", + "grDevices", + "grid", + "gtable", + "isoband", + "lifecycle", + "mgcv", + "rlang", + "scales", + "stats", + "tibble", + "vctrs", + "withr" + ], + "Hash": "44c6a2f8202d5b7e878ea274b1092426" + }, + "globals": { + "Package": "globals", + "Version": "0.16.3", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "R", + "codetools" + ], + "Hash": "2580567908cafd4f187c1e5a91e98b7f" + }, "glue": { "Package": "glue", - 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"Version": "0.5.4", + "Version": "0.5.8.1", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R", "base64enc", "digest", - "ellipsis", "fastmap", "grDevices", "rlang", "utils" ], - "Hash": "9d27e99cc90bd701c0a7a63e5923f9b7" + "Hash": "81d371a9cc60640e74e4ab6ac46dcedc" }, "htmlwidgets": { "Package": "htmlwidgets", - "Version": "1.6.1", + "Version": "1.6.4", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -523,11 +620,11 @@ "rmarkdown", "yaml" ], - "Hash": "b677ee5954471eaa974c0d099a343a1a" + "Hash": "04291cc45198225444a397606810ac37" }, "httpuv": { "Package": "httpuv", - "Version": "1.6.9", + "Version": "1.6.15", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -538,11 +635,11 @@ "promises", "utils" ], - "Hash": "1046aa31a57eae8b357267a56a0b6d8b" + "Hash": "d55aa087c47a63ead0f6fc10f8fa1ee0" }, "httr": { "Package": "httr", - "Version": "1.4.5", + "Version": "1.4.7", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -553,30 +650,62 @@ "mime", "openssl" ], - 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"Version": "1.8.4", + "Version": "1.8.9", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "methods" ], - "Hash": "a4269a09a9b865579b2635c77e572374" + "Hash": "4e993b65c2c3ffbffce7bb3e2c6f832b" }, "knitr": { "Package": "knitr", - "Version": "1.42", + "Version": "1.48", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -612,22 +741,33 @@ "xfun", "yaml" ], - "Hash": "8329a9bcc82943c8069104d4be3ee22d" + "Hash": "acf380f300c721da9fde7df115a5f86f" + }, + "labeling": { + "Package": "labeling", + "Version": "0.4.3", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "graphics", + "stats" + ], + "Hash": "b64ec208ac5bc1852b285f665d6368b3" }, "later": { "Package": "later", - "Version": "1.3.0", + "Version": "1.3.2", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "Rcpp", "rlang" ], - "Hash": "7e7b457d7766bc47f2a5f21cc2984f8e" + "Hash": "a3e051d405326b8b0012377434c62b37" }, "lattice": { "Package": "lattice", - "Version": "0.20-45", + "Version": "0.22-6", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -638,7 +778,7 @@ "stats", "utils" ], - "Hash": "b64cdbb2b340437c4ee047a1f4c4377b" + "Hash": "cc5ac1ba4c238c7ca9fa6a87ca11a7e2" }, "lazyeval": { "Package": "lazyeval", @@ -652,7 +792,7 @@ }, "lifecycle": { "Package": "lifecycle", - "Version": "1.0.3", + "Version": "1.0.4", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -661,7 +801,17 @@ "glue", "rlang" ], - "Hash": "001cecbeac1cff9301bdc3775ee46a86" + "Hash": "b8552d117e1b808b09a832f589b79035" + }, + "listenv": { + "Package": "listenv", + "Version": "0.9.1", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "R" + ], + "Hash": "e2fca3e12e4db979dccc6e519b10a7ee" }, "magrittr": { "Package": "magrittr", @@ -684,6 +834,23 @@ ], "Hash": "e2817ccf4a065c5d9d7f2cfbe7c1d78c" }, + "mgcv": { + "Package": "mgcv", + "Version": "1.9-1", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "Matrix", + "R", + "graphics", + "methods", + "nlme", + "splines", + "stats", + "utils" + ], + "Hash": "110ee9d83b496279960e162ac97764ce" + }, "mime": { "Package": "mime", "Version": "0.12", @@ -694,6 +861,17 @@ ], "Hash": "18e9c28c1d3ca1560ce30658b22ce104" }, + "munsell": { + "Package": "munsell", + "Version": "0.5.1", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "colorspace", + "methods" + ], + "Hash": "4fd8900853b746af55b81fda99da7695" + }, "networkD3": { "Package": "networkD3", "Version": "0.4", @@ -707,14 +885,45 @@ ], "Hash": "38310ec4ddb1398359abdd603c151067" }, + "nlme": { + "Package": "nlme", + "Version": "3.1-166", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "R", + "graphics", + "lattice", + "stats", + "utils" + ], + "Hash": "ccbb8846be320b627e6aa2b4616a2ded" + }, "openssl": { "Package": "openssl", - "Version": "2.1.1", - "Source": "Repository" + "Version": "2.2.2", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "askpass" + ], + "Hash": "d413e0fef796c9401a4419485f709ca1" + }, + "parallelly": { + "Package": "parallelly", + "Version": "1.38.0", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "parallel", + "tools", + "utils" + ], + "Hash": "6e8b139c1904f5e9e14c69db64453bbe" }, "pillar": { "Package": "pillar", - "Version": "1.8.1", + "Version": "1.9.0", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -727,7 +936,22 @@ "utils", "vctrs" ], - "Hash": "f2316df30902c81729ae9de95ad5a608" + "Hash": "15da5a8412f317beeee6175fbc76f4bb" + }, + "pkgbuild": { + "Package": "pkgbuild", + "Version": "1.4.5", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "R", + "R6", + "callr", + "cli", + "desc", + "processx" + ], + "Hash": "30eaaab94db72652e72e3475c1b55278" }, "pkgconfig": { "Package": "pkgconfig", @@ -741,23 +965,25 @@ }, "pkgload": { "Package": "pkgload", - "Version": "1.3.2", + "Version": "1.4.0", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R", "cli", - "crayon", "desc", "fs", "glue", + "lifecycle", "methods", + "pkgbuild", + "processx", "rlang", "rprojroot", "utils", "withr" ], - "Hash": "6b0c222c5071efe0f3baf3dae9aa40e2" + "Hash": "2ec30ffbeec83da57655b850cf2d3e0e" }, "png": { "Package": "png", @@ -778,14 +1004,17 @@ }, "prettyunits": { "Package": "prettyunits", - "Version": "1.1.1", + "Version": "1.2.0", "Source": "Repository", "Repository": "CRAN", - "Hash": "95ef9167b75dde9d2ccc3c7528393e7e" + "Requirements": [ + "R" + ], + "Hash": "6b01fc98b1e86c4f705ce9dcfd2f57c7" }, "processx": { "Package": "processx", - "Version": "3.8.0", + "Version": "3.8.4", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -794,50 +1023,52 @@ "ps", "utils" ], - "Hash": "a33ee2d9bf07564efb888ad98410da84" + "Hash": "0c90a7d71988856bad2a2a45dd871bb9" }, "progress": { "Package": "progress", - "Version": "1.2.2", + "Version": "1.2.3", "Source": "Repository", "Repository": "CRAN", "Requirements": [ + "R", "R6", "crayon", "hms", "prettyunits" ], - "Hash": "14dc9f7a3c91ebb14ec5bb9208a07061" + "Hash": "f4625e061cb2865f111b47ff163a5ca6" }, "promises": { "Package": "promises", - "Version": "1.2.0.1", + "Version": "1.3.0", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R6", "Rcpp", + "fastmap", "later", "magrittr", "rlang", "stats" ], - "Hash": "4ab2c43adb4d4699cf3690acd378d75d" + "Hash": "434cd5388a3979e74be5c219bcd6e77d" }, "ps": { "Package": "ps", - "Version": "1.7.2", + "Version": "1.8.1", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R", "utils" ], - "Hash": "68dd03d98a5efd1eb3012436de45ba83" + "Hash": "b4404b1de13758dea1c0484ad0d48563" }, "purrr": { "Package": "purrr", - "Version": "1.0.1", + "Version": "1.0.2", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -848,7 +1079,7 @@ "rlang", "vctrs" ], - "Hash": "d71c815267c640f17ddbf7f16144b4bb" + "Hash": "1cba04a4e9414bdefc9dcaa99649a8dc" }, "r2d3": { "Package": "r2d3", @@ -876,7 +1107,7 @@ }, "readr": { "Package": "readr", - "Version": "2.1.4", + "Version": "2.1.5", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -895,7 +1126,7 @@ "utils", "vroom" ], - "Hash": "b5047343b3825f37ad9d3b5d89aa1078" + "Hash": "9de96463d2117f6ac49980577939dfb3" }, "rematch2": { "Package": "rematch2", @@ -909,14 +1140,14 @@ }, "renv": { "Package": "renv", - "Version": "0.17.3", + "Version": "1.0.11", "OS_type": null, - "Repository": "CRAN", + "Repository": "binaries", "Source": "Repository" }, "reticulate": { "Package": "reticulate", - "Version": "1.28", + "Version": "1.39.0", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -930,69 +1161,66 @@ "methods", "png", "rappdirs", + "rlang", "utils", "withr" ], - "Hash": "86c441bf33e1d608db773cb94b848458" + "Hash": "e1a5d04397edc1580c5e0ed1dbdccf76" }, - "rex": { - "Package": "rex", - "Version": "1.2.1", + "rlang": { + "Package": "rlang", + "Version": "1.1.4", "Source": "Repository", "Repository": "CRAN", "Requirements": [ - "lazyeval" + "R", + "utils" ], - "Hash": "ae34cd56890607370665bee5bd17812f" - }, - "rlang": { - "Package": "rlang", - "Version": "1.1.3", - "Source": "Repository" + "Hash": "3eec01f8b1dee337674b2e34ab1f9bc1" }, "rmarkdown": { "Package": "rmarkdown", - "Version": "2.20", + "Version": "2.28", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R", "bslib", "evaluate", + "fontawesome", "htmltools", "jquerylib", "jsonlite", "knitr", "methods", - "stringr", "tinytex", "tools", "utils", "xfun", "yaml" ], - "Hash": "716fde5382293cc94a71f68c85b78d19" + "Hash": "062470668513dcda416927085ee9bdc7" }, "rprojroot": { "Package": "rprojroot", - "Version": "2.0.3", + "Version": "2.0.4", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R" ], - "Hash": "1de7ab598047a87bba48434ba35d497d" + "Hash": "4c8415e0ec1e29f3f4f6fc108bef0144" }, "rstudioapi": { "Package": "rstudioapi", - "Version": "0.14", + "Version": "0.17.1", "Source": "Repository", "Repository": "CRAN", - "Hash": "690bd2acc42a9166ce34845884459320" + "Hash": "5f90cd73946d706cfe26024294236113" }, "sass": { "Package": "sass", - "Version": "0.4.5", + "Version": "0.4.9", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -1002,11 +1230,31 @@ "rappdirs", "rlang" ], - "Hash": "2bb4371a4c80115518261866eab6ab11" + "Hash": "d53dbfddf695303ea4ad66f86e99b95d" + }, + "scales": { + "Package": "scales", + "Version": "1.3.0", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "R", + "R6", + "RColorBrewer", + "cli", + "farver", + "glue", + "labeling", + "lifecycle", + "munsell", + "rlang", + "viridisLite" + ], + "Hash": "c19df082ba346b0ffa6f833e92de34d1" }, "shiny": { "Package": "shiny", - "Version": "1.7.4", + "Version": "1.9.1", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -1016,7 +1264,6 @@ "cachem", "commonmark", "crayon", - "ellipsis", "fastmap", "fontawesome", "glue", @@ -1036,7 +1283,7 @@ "withr", "xtable" ], - "Hash": "c2eae3d8c670fa9dfa35a12066f4a1d5" + "Hash": "6a293995a66e12c48d13aa1f957d09c7" }, "shinydashboard": { "Package": "shinydashboard", @@ -1070,7 +1317,8 @@ "shiny", "shinydashboard", "waiter" - ] + ], + "Hash": "5ac2268c276ed8481cc1780a6b6cbb8d" }, "shinyjs": { "Package": "shinyjs", @@ -1085,15 +1333,39 @@ ], "Hash": "802e4786b353a4bb27116957558548d5" }, + "shinyloadtest": { + "Package": "shinyloadtest", + "Version": "1.2.0", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "R", + "R6", + "cli", + "curl", + "dplyr", + "ggplot2", + "httpuv", + "jsonlite", + "magrittr", + "rlang", + "scales", + "stringr", + "svglite", + "vroom", + "websocket", + "xml2" + ], + "Hash": "0e63156a8b6abe5dad29a344e3ad797f" + }, "shinypop": { "Package": "shinypop", "Version": "0.1.1", "Source": "GitHub", "RemoteType": "github", "RemoteHost": "api.github.com", - "RemoteUsername": "dreamRs", "RemoteRepo": "shinypop", - "RemoteRef": "master", + "RemoteUsername": "dreamrs", "RemoteSha": "7745a0b1ecf31f783fa59603f3c5cede0c948118", "Requirements": [ "R", @@ -1101,7 +1373,7 @@ "jsonlite", "shiny" ], - "Hash": "ee29555190ce6a726046a5909cc91d9b" + "Hash": "d69a5eada8b146d064f367d650b9f2cd" }, "shinythemes": { "Package": "shinythemes", @@ -1126,7 +1398,7 @@ }, "stringi": { "Package": "stringi", - "Version": "1.7.12", + "Version": "1.8.4", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -1135,11 +1407,11 @@ "tools", "utils" ], - "Hash": "ca8bd84263c77310739d2cf64d84d7c9" + "Hash": "39e1144fd75428983dc3f63aa53dfa91" }, "stringr": { "Package": "stringr", - "Version": "1.5.0", + "Version": "1.5.1", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -1152,18 +1424,42 @@ "stringi", "vctrs" ], - "Hash": "671a4d384ae9d32fc47a14e98bfa3dc8" + "Hash": "960e2ae9e09656611e0b8214ad543207" + }, + "svglite": { + "Package": "svglite", + "Version": "2.1.3", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "R", + "cpp11", + "systemfonts" + ], + "Hash": "124a41fdfa23e8691cb744c762f10516" }, "sys": { "Package": "sys", - "Version": "3.4.1", + "Version": "3.4.3", "Source": "Repository", "Repository": "CRAN", - "Hash": "34c16f1ef796057bfa06d3f4ff818a5d" + "Hash": "de342ebfebdbf40477d0758d05426646" + }, + "systemfonts": { + "Package": "systemfonts", + "Version": "1.1.0", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "R", + "cpp11", + "lifecycle" + ], + "Hash": "213b6b8ed5afbf934843e6c3b090d418" }, "testthat": { "Package": "testthat", - "Version": "3.1.6", + "Version": "3.2.1.1", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -1174,7 +1470,6 @@ "cli", "desc", "digest", - "ellipsis", "evaluate", "jsonlite", "lifecycle", @@ -1189,11 +1484,11 @@ "waldo", "withr" ], - "Hash": "7910146255835c66e9eb272fb215248d" + "Hash": "3f6e7e5e2220856ff865e4834766bf2b" }, "tibble": { "Package": "tibble", - "Version": "3.1.8", + "Version": "3.2.1", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -1208,11 +1503,11 @@ "utils", "vctrs" ], - "Hash": "56b6934ef0f8c68225949a8672fe1a8f" + "Hash": "a84e2cc86d07289b3b6f5069df7a004c" }, "tidyr": { "Package": "tidyr", - "Version": "1.3.0", + "Version": "1.3.1", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -1231,11 +1526,11 @@ "utils", "vctrs" ], - "Hash": "e47debdc7ce599b070c8e78e8ac0cfcf" + "Hash": "915fb7ce036c22a6a33b5a8adb712eb1" }, "tidyselect": { "Package": "tidyselect", - "Version": "1.2.0", + "Version": "1.2.1", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -1247,42 +1542,42 @@ "vctrs", "withr" ], - "Hash": "79540e5fcd9e0435af547d885f184fd5" + "Hash": "829f27b9c4919c16b593794a6344d6c0" }, "tinytex": { "Package": "tinytex", - "Version": "0.44", + "Version": "0.53", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "xfun" ], - "Hash": "c0f007e2eeed7722ce13d42b84a22e07" + "Hash": "9db859e8aabbb474293dde3097839420" }, "tzdb": { "Package": "tzdb", - "Version": "0.3.0", + "Version": "0.4.0", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R", "cpp11" ], - "Hash": "b2e1cbce7c903eaf23ec05c58e59fb5e" + "Hash": "f561504ec2897f4d46f0c7657e488ae1" }, "utf8": { "Package": "utf8", - "Version": "1.2.3", + "Version": "1.2.4", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R" ], - "Hash": "1fe17157424bb09c48a8b3b550c753bc" + "Hash": "62b65c52671e6665f803ff02954446e9" }, "vctrs": { "Package": "vctrs", - "Version": "0.5.2", + "Version": "0.6.5", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -1292,11 +1587,21 @@ "lifecycle", "rlang" ], - "Hash": "e4ffa94ceed5f124d429a5a5f0f5b378" + "Hash": "c03fa420630029418f7e6da3667aac4a" + }, + "viridisLite": { + "Package": "viridisLite", + "Version": "0.4.2", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "R" + ], + "Hash": "c826c7c4241b6fc89ff55aaea3fa7491" }, "vroom": { "Package": "vroom", - "Version": "1.6.1", + "Version": "1.6.5", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -1318,7 +1623,7 @@ "vctrs", "withr" ], - "Hash": "7015a74373b83ffaef64023f4a0f5033" + "Hash": "390f9315bc0025be03012054103d227c" }, "waiter": { "Package": "waiter", @@ -1334,55 +1639,71 @@ }, "waldo": { "Package": "waldo", - "Version": "0.4.0", + "Version": "0.5.3", "Source": "Repository", "Repository": "CRAN", "Requirements": [ + "R", "cli", "diffobj", - "fansi", "glue", "methods", "rematch2", "rlang", "tibble" ], - "Hash": "035fba89d0c86e2113120f93301b98ad" + "Hash": "16aa934a49658677d8041df9017329b9" + }, + "websocket": { + "Package": "websocket", + "Version": "1.4.2", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "AsioHeaders", + "R6", + "cpp11", + "later" + ], + "Hash": "e77c5569354172d0d04d54a9dec89e33" }, "withr": { "Package": "withr", - "Version": "2.5.0", + "Version": "3.0.2", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R", "grDevices", - "graphics", - "stats" + "graphics" ], - "Hash": "c0e49a9760983e81e55cdd9be92e7182" + "Hash": "cc2d62c76458d425210d1eb1478b30b4" }, "xfun": { "Package": "xfun", - "Version": "0.37", + "Version": "0.48", "Source": "Repository", "Repository": "CRAN", "Requirements": [ + "R", + "grDevices", "stats", "tools" ], - "Hash": "a6860e1400a8fd1ddb6d9b4230cc34ab" + "Hash": "89e455b87c84e227eb7f60a1b4e5fe1f" }, "xml2": { "Package": "xml2", - "Version": "1.3.3", + "Version": "1.3.6", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R", - "methods" + "cli", + "methods", + "rlang" ], - "Hash": "40682ed6a969ea5abfd351eb67833adc" + "Hash": "1d0336142f4cd25d8d23cd3ba7a8fb61" }, "xtable": { "Package": "xtable", @@ -1398,10 +1719,10 @@ }, "yaml": { "Package": "yaml", - "Version": "2.3.7", + "Version": "2.3.10", "Source": "Repository", "Repository": "CRAN", - "Hash": "0d0056cc5383fbc240ccd0cb584bf436" + "Hash": "51dab85c6c98e50a18d7551e9d49f76c" } } } diff --git a/renv/activate.R b/renv/activate.R index d77c4c83..0eb51088 100644 --- a/renv/activate.R +++ b/renv/activate.R @@ -2,10 +2,28 @@ local({ # the requested version of renv - version <- "0.17.3" + version <- "1.0.11" + attr(version, "sha") <- NULL # the project directory - project <- getwd() + 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({ @@ -15,6 +33,14 @@ local({ 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 # TODO: prefer using the configuration one in the future envvars <- c( @@ -34,9 +60,22 @@ local({ }) - if (!enabled) + # 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") @@ -59,22 +98,154 @@ local({ 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;;ide:help:\\1\a?\\1\033]8;;\a`" + text <- gsub(pattern, replacement, text, perl = TRUE) + + # runnable code + pattern <- "`(renv::(?:[^`])+)`" + replacement <- "`\033]8;;ide: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.environment(x) || length(x)) x else 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) + + } + + startswith <- function(string, prefix) { + substring(string, 1, nchar(prefix)) == prefix } bootstrap <- function(version, library) { + friendly <- renv_bootstrap_version_friendly(version) + section <- header(sprintf("Bootstrapping renv %s", friendly)) + catf(section) + # attempt to download renv - tarball <- tryCatch(renv_bootstrap_download(version), error = identity) - if (inherits(tarball, "error")) - stop("failed to download renv ", version) + 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 - status <- tryCatch(renv_bootstrap_install(version, tarball, library), error = identity) - if (inherits(status, "error")) - stop("failed to install renv ", version) + 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() { @@ -83,31 +254,32 @@ local({ 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)) + 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) - # if we're testing, re-use the test repositories - if (renv_bootstrap_tests_running()) { - repos <- getOption("renv.tests.repos") - if (!is.null(repos)) - return(repos) - } - # retrieve current repos repos <- getOption("repos") # ensure @CRAN@ entries are resolved - repos[repos == "@CRAN@"] <- getOption( - "renv.repos.cran", - "https://cloud.r-project.org" - ) + repos[repos == "@CRAN@"] <- cran # add in renv.bootstrap.repos if set default <- c(FALLBACK = "https://cloud.r-project.org") @@ -146,33 +318,34 @@ local({ renv_bootstrap_download <- function(version) { - # if the renv version number has 4 components, assume it must - # be retrieved via github - nv <- numeric_version(version) - components <- unclass(nv)[[1]] - - # if this appears to be a development version of 'renv', we'll - # try to restore from github - dev <- length(components) == 4L - - # begin collecting different methods for finding renv - methods <- c( - renv_bootstrap_download_tarball, - if (dev) - renv_bootstrap_download_github - else c( - renv_bootstrap_download_cran_latest, - renv_bootstrap_download_cran_archive + 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(version), error = identity) + path <- tryCatch(method(), error = identity) if (is.character(path) && file.exists(path)) return(path) } - stop("failed to download renv ", version) + stop("All download methods failed") } @@ -195,8 +368,11 @@ local({ quiet = TRUE ) - if ("headers" %in% names(formals(utils::download.file))) - args$headers <- renv_bootstrap_download_custom_headers(url) + if ("headers" %in% names(formals(utils::download.file))) { + headers <- renv_bootstrap_download_custom_headers(url) + if (length(headers) && is.character(headers)) + args$headers <- headers + } do.call(utils::download.file, args) @@ -236,8 +412,6 @@ local({ type <- spec$type repos <- spec$repos - message("* Downloading renv ", version, " ... ", appendLF = FALSE) - baseurl <- utils::contrib.url(repos = repos, type = type) ext <- if (identical(type, "source")) ".tar.gz" @@ -254,13 +428,10 @@ local({ condition = identity ) - if (inherits(status, "condition")) { - message("FAILED") + if (inherits(status, "condition")) return(FALSE) - } # report success and return - message("OK (downloaded ", type, ")") destfile } @@ -280,10 +451,21 @@ local({ 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( - utils::available.packages(type = type, repos = repos), + do.call(utils::available.packages, args), stringsAsFactors = FALSE ), error = identity @@ -317,8 +499,6 @@ local({ urls <- file.path(repos, "src/contrib/Archive/renv", name) destfile <- file.path(tempdir(), name) - message("* Downloading renv ", version, " ... ", appendLF = FALSE) - for (url in urls) { status <- tryCatch( @@ -326,14 +506,11 @@ local({ condition = identity ) - if (identical(status, 0L)) { - message("OK") + if (identical(status, 0L)) return(destfile) - } } - message("FAILED") return(FALSE) } @@ -356,7 +533,7 @@ local({ 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." + fmt <- "- RENV_BOOTSTRAP_TARBALL is set (%s) but does not exist." msg <- sprintf(fmt, tarball) warning(msg) @@ -365,14 +542,19 @@ local({ } - fmt <- "* Bootstrapping with tarball at path '%s'." - msg <- sprintf(fmt, tarball) - message(msg) - + 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") @@ -380,23 +562,21 @@ local({ return(FALSE) # prepare download options - pat <- Sys.getenv("GITHUB_PAT") - if (nzchar(Sys.which("curl")) && nzchar(pat)) { + token <- renv_bootstrap_github_token() + if (nzchar(Sys.which("curl")) && nzchar(token)) { fmt <- "--location --fail --header \"Authorization: token %s\"" - extra <- sprintf(fmt, pat) + 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(pat)) { + } else if (nzchar(Sys.which("wget")) && nzchar(token)) { fmt <- "--header=\"Authorization: token %s\"" - extra <- sprintf(fmt, pat) + 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) } - message("* Downloading renv ", version, " from GitHub ... ", appendLF = FALSE) - url <- file.path("https://api.github.com/repos/rstudio/renv/tarball", version) name <- sprintf("renv_%s.tar.gz", version) destfile <- file.path(tempdir(), name) @@ -406,26 +586,105 @@ local({ condition = identity ) - if (!identical(status, 0L)) { - message("FAILED") + if (!identical(status, 0L)) return(FALSE) - } - message("OK") + 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 - message("* Installing renv ", version, " ... ", appendLF = FALSE) 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) + R <- file.path(bin, exe) args <- c( "--vanilla", "CMD", "INSTALL", "--no-multiarch", @@ -433,19 +692,7 @@ local({ shQuote(path.expand(tarball)) ) - output <- system2(r, args, stdout = TRUE, stderr = TRUE) - message("Done!") - - # check for successful install - status <- attr(output, "status") - if (is.numeric(status) && !identical(status, 0L)) { - header <- "Error installing renv:" - lines <- paste(rep.int("=", nchar(header)), collapse = "") - text <- c(header, lines, output) - writeLines(text, con = stderr()) - } - - status + system2(R, args, stdout = TRUE, stderr = TRUE) } @@ -486,6 +733,9 @@ local({ # 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()) @@ -655,34 +905,61 @@ local({ } - renv_bootstrap_validate_version <- function(version) { + renv_bootstrap_validate_version <- function(version, description = NULL) { - loadedversion <- utils::packageDescription("renv", fields = "Version") - if (version == loadedversion) + # 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) - # assume four-component versions are from GitHub; - # three-component versions are from CRAN - components <- strsplit(loadedversion, "[.-]")[[1]] - remote <- if (length(components) == 4L) - paste("rstudio/renv", loadedversion, sep = "@") + # 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", loadedversion, sep = "@") + paste("renv", description[["Version"]], sep = "@") - fmt <- paste( - "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.", - sep = "\n" + # display both loaded version + sha if available + friendly <- renv_bootstrap_version_friendly( + version = description[["Version"]], + sha = if (dev) description[["RemoteSha"]] ) - msg <- sprintf(fmt, loadedversion, version, remote) - warning(msg, call. = FALSE) + 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"]] + is.character(expected) && startswith(expected, version) + } + + 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-") @@ -706,7 +983,7 @@ local({ hooks <- getHook("renv::autoload") for (hook in hooks) if (is.function(hook)) - tryCatch(hook(), error = warning) + tryCatch(hook(), error = warnify) # load the project renv::load(project) @@ -847,6 +1124,40 @@ local({ } + 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(version, libpath) + } + + renv_bootstrap_run <- function(version, libpath) { + + # 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 = getwd())) + } + + # 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) { @@ -855,7 +1166,7 @@ local({ # if jsonlite is loaded, use that instead if ("jsonlite" %in% loadedNamespaces()) { - json <- catch(renv_json_read_jsonlite(file, text)) + json <- tryCatch(renv_json_read_jsonlite(file, text), error = identity) if (!inherits(json, "error")) return(json) @@ -864,7 +1175,7 @@ local({ } # otherwise, fall back to the default JSON reader - json <- catch(renv_json_read_default(file, text)) + json <- tryCatch(renv_json_read_default(file, text), error = identity) if (!inherits(json, "error")) return(json) @@ -877,14 +1188,14 @@ local({ } renv_json_read_jsonlite <- function(file = NULL, text = NULL) { - text <- paste(text %||% read(file), collapse = "\n") + text <- paste(text %||% readLines(file, warn = FALSE), collapse = "\n") jsonlite::fromJSON(txt = text, simplifyVector = FALSE) } renv_json_read_default <- function(file = NULL, text = NULL) { # find strings in the JSON - text <- paste(text %||% read(file), collapse = "\n") + text <- paste(text %||% readLines(file, warn = FALSE), collapse = "\n") pattern <- '["](?:(?:\\\\.)|(?:[^"\\\\]))*?["]' locs <- gregexpr(pattern, text, perl = TRUE)[[1]] @@ -932,14 +1243,14 @@ local({ map <- as.list(map) # remap strings in object - remapped <- renv_json_remap(json, map) + remapped <- renv_json_read_remap(json, map) # evaluate eval(remapped, envir = baseenv()) } - renv_json_remap <- function(json, map) { + renv_json_read_remap <- function(json, map) { # fix names if (!is.null(names(json))) { @@ -966,7 +1277,7 @@ local({ # recurse if (is.recursive(json)) { for (i in seq_along(json)) { - json[i] <- list(renv_json_remap(json[[i]], map)) + json[i] <- list(renv_json_read_remap(json[[i]], map)) } } @@ -986,35 +1297,9 @@ local({ # construct full libpath libpath <- file.path(root, prefix) - # attempt to load - if (renv_bootstrap_load(project, libpath, version)) - return(TRUE) - - # load failed; inform user we're about to bootstrap - prefix <- paste("# Bootstrapping renv", version) - postfix <- paste(rep.int("-", 77L - nchar(prefix)), collapse = "") - header <- paste(prefix, postfix) - message(header) - - # 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)) { - message("* Successfully installed and loaded renv ", version, ".") - return(renv::load()) - } - - # 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." - ) + # run bootstrap code + renv_bootstrap_exec(project, libpath, version) - warning(paste(msg, collapse = "\n"), call. = FALSE) + invisible() })