From bd2a1a5fd84a5f939562a7ae2beefff624b0574b Mon Sep 17 00:00:00 2001 From: Dave Mills Date: Thu, 17 Oct 2024 11:36:33 +0100 Subject: [PATCH] renv update properly --- renv.lock | 857 +++++++++++++++++++++++++++++++++++++++- renv/activate.R | 945 ++++++++------------------------------------- renv/settings.json | 19 + 3 files changed, 1029 insertions(+), 792 deletions(-) create mode 100644 renv/settings.json diff --git a/renv.lock b/renv.lock index 73319bd..3c2e39f 100644 --- a/renv.lock +++ b/renv.lock @@ -8,5 +8,860 @@ } ] }, - "Packages": {} + "Packages": { + "DBI": { + "Package": "DBI", + "Version": "1.2.3", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "065ae649b05f1ff66bb0c793107508f5" + }, + "DT": { + "Package": "DT", + "Version": "0.33", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "64ff3427f559ce3f2597a4fe13255cb6" + }, + "MASS": { + "Package": "MASS", + "Version": "7.3-61", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "0cafd6f0500e5deba33be22c46bf6055" + }, + "Matrix": { + "Package": "Matrix", + "Version": "1.7-0", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "1920b2f11133b12350024297d8a4ff4a" + }, + "R6": { + "Package": "R6", + "Version": "2.5.1", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "470851b6d5d0ac559e9d01bb352b4021" + }, + "RColorBrewer": { + "Package": "RColorBrewer", + "Version": "1.1-3", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "45f0398006e83a5b10b72a90663d8d8c" + }, + "Rcpp": { + "Package": "Rcpp", + "Version": "1.0.13", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "f27411eb6d9c3dada5edd444b8416675" + }, + "askpass": { + "Package": "askpass", + "Version": "1.2.1", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "c39f4155b3ceb1a9a2799d700fbd4b6a" + }, + "backports": { + "Package": "backports", + "Version": "1.5.0", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "e1e1b9d75c37401117b636b7ae50827a" + }, + "base64enc": { + "Package": "base64enc", + "Version": "0.1-3", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "543776ae6848fde2f48ff3816d0628bc" + }, + "bit": { + "Package": "bit", + "Version": "4.5.0", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "5dc7b2677d65d0e874fc4aaf0e879987" + }, + "bit64": { + "Package": "bit64", + "Version": "4.5.2", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "e84984bf5f12a18628d9a02322128dfd" + }, + "blob": { + "Package": "blob", + "Version": "1.2.4", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "40415719b5a479b87949f3aa0aee737c" + }, + "broom": { + "Package": "broom", + "Version": "1.0.7", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "8fcc818f3b9887aebaf206f141437cc9" + }, + "bslib": { + "Package": "bslib", + "Version": "0.8.0", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "b299c6741ca9746fb227debcb0f9fb6c" + }, + "cachem": { + "Package": "cachem", + "Version": "1.1.0", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "cd9a672193789068eb5a2aad65a0dedf" + }, + "callr": { + "Package": "callr", + "Version": "3.7.6", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "d7e13f49c19103ece9e58ad2d83a7354" + }, + "cellranger": { + "Package": "cellranger", + "Version": "1.1.0", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "f61dbaec772ccd2e17705c1e872e9e7c" + }, + "cli": { + "Package": "cli", + "Version": "3.6.3", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "b21916dd77a27642b447374a5d30ecf3" + }, + "clipr": { + "Package": "clipr", + "Version": "0.8.0", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "3f038e5ac7f41d4ac41ce658c85e3042" + }, + "colorspace": { + "Package": "colorspace", + "Version": "2.1-1", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "d954cb1c57e8d8b756165d7ba18aa55a" + }, + "commonmark": { + "Package": "commonmark", + "Version": "1.9.2", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "14eb0596f987c71535d07c3aff814742" + }, + "conflicted": { + "Package": "conflicted", + "Version": "1.2.0", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "bb097fccb22d156624fd07cd2894ddb6" + }, + "cpp11": { + "Package": "cpp11", + "Version": "0.5.0", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "91570bba75d0c9d3f1040c835cee8fba" + }, + "crayon": { + "Package": "crayon", + "Version": "1.5.3", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "859d96e65ef198fd43e82b9628d593ef" + }, + "crosstalk": { + "Package": "crosstalk", + "Version": "1.2.1", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "ab12c7b080a57475248a30f4db6298c0" + }, + "curl": { + "Package": "curl", + "Version": "5.2.3", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "d91263322a58af798f6cf3b13fd56dde" + }, + "data.table": { + "Package": "data.table", + "Version": "1.16.2", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "2e00b378fc3be69c865120d9f313039a" + }, + "dbplyr": { + "Package": "dbplyr", + "Version": "2.5.0", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "39b2e002522bfd258039ee4e889e0fd1" + }, + "digest": { + "Package": "digest", + "Version": "0.6.37", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "33698c4b3127fc9f506654607fb73676" + }, + "dplyr": { + "Package": "dplyr", + "Version": "1.1.4", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "fedd9d00c2944ff00a0e2696ccf048ec" + }, + "dtplyr": { + "Package": "dtplyr", + "Version": "1.3.1", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "54ed3ea01b11e81a86544faaecfef8e2" + }, + "evaluate": { + "Package": "evaluate", + "Version": "1.0.1", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "3fd29944b231036ad67c3edb32e02201" + }, + "fansi": { + "Package": "fansi", + "Version": "1.0.6", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "962174cf2aeb5b9eea581522286a911f" + }, + "farver": { + "Package": "farver", + "Version": "2.1.2", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "680887028577f3fa2a81e410ed0d6e42" + }, + "fastmap": { + "Package": "fastmap", + "Version": "1.2.0", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "aa5e1cd11c2d15497494c5292d7ffcc8" + }, + "fontawesome": { + "Package": "fontawesome", + "Version": "0.5.2", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "c2efdd5f0bcd1ea861c2d4e2a883a67d" + }, + "forcats": { + "Package": "forcats", + "Version": "1.0.0", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "1a0a9a3d5083d0d573c4214576f1e690" + }, + "fs": { + "Package": "fs", + "Version": "1.6.4", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "15aeb8c27f5ea5161f9f6a641fafd93a" + }, + "gargle": { + "Package": "gargle", + "Version": "1.5.2", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "fc0b272e5847c58cd5da9b20eedbd026" + }, + "generics": { + "Package": "generics", + "Version": "0.1.3", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "15e9634c0fcd294799e9b2e929ed1b86" + }, + "ggplot2": { + "Package": "ggplot2", + "Version": "3.5.1", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "44c6a2f8202d5b7e878ea274b1092426" + }, + "glue": { + "Package": "glue", + "Version": "1.8.0", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "5899f1eaa825580172bb56c08266f37c" + }, + "googledrive": { + "Package": "googledrive", + "Version": "2.1.1", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "e99641edef03e2a5e87f0a0b1fcc97f4" + }, + "googlesheets4": { + "Package": "googlesheets4", + "Version": "1.1.1", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "d6db1667059d027da730decdc214b959" + }, + "gtable": { + "Package": "gtable", + "Version": "0.3.5", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "e18861963cbc65a27736e02b3cd3c4a0" + }, + "haven": { + "Package": "haven", + "Version": "2.5.4", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "9171f898db9d9c4c1b2c745adc2c1ef1" + }, + "highr": { + "Package": "highr", + "Version": "0.11", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "d65ba49117ca223614f71b60d85b8ab7" + }, + "hms": { + "Package": "hms", + "Version": "1.1.3", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "b59377caa7ed00fa41808342002138f9" + }, + "htmltools": { + "Package": "htmltools", + "Version": "0.5.8.1", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "81d371a9cc60640e74e4ab6ac46dcedc" + }, + "htmlwidgets": { + "Package": "htmlwidgets", + "Version": "1.6.4", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "04291cc45198225444a397606810ac37" + }, + "httpuv": { + "Package": "httpuv", + "Version": "1.6.15", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "d55aa087c47a63ead0f6fc10f8fa1ee0" + }, + "httr": { + "Package": "httr", + "Version": "1.4.7", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "ac107251d9d9fd72f0ca8049988f1d7f" + }, + "ids": { + "Package": "ids", + "Version": "1.0.1", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "99df65cfef20e525ed38c3d2577f7190" + }, + "isoband": { + "Package": "isoband", + "Version": "0.2.7", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "0080607b4a1a7b28979aecef976d8bc2" + }, + "jquerylib": { + "Package": "jquerylib", + "Version": "0.1.4", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "5aab57a3bd297eee1c1d862735972182" + }, + "jsonlite": { + "Package": "jsonlite", + "Version": "1.8.9", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "4e993b65c2c3ffbffce7bb3e2c6f832b" + }, + "knitr": { + "Package": "knitr", + "Version": "1.48", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "acf380f300c721da9fde7df115a5f86f" + }, + "labeling": { + "Package": "labeling", + "Version": "0.4.3", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "b64ec208ac5bc1852b285f665d6368b3" + }, + "later": { + "Package": "later", + "Version": "1.3.2", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "a3e051d405326b8b0012377434c62b37" + }, + "lattice": { + "Package": "lattice", + "Version": "0.22-6", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "cc5ac1ba4c238c7ca9fa6a87ca11a7e2" + }, + "lazyeval": { + "Package": "lazyeval", + "Version": "0.2.2", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "d908914ae53b04d4c0c0fd72ecc35370" + }, + "lifecycle": { + "Package": "lifecycle", + "Version": "1.0.4", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "b8552d117e1b808b09a832f589b79035" + }, + "lubridate": { + "Package": "lubridate", + "Version": "1.9.3", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "680ad542fbcf801442c83a6ac5a2126c" + }, + "magrittr": { + "Package": "magrittr", + "Version": "2.0.3", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "7ce2733a9826b3aeb1775d56fd305472" + }, + "memoise": { + "Package": "memoise", + "Version": "2.0.1", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "e2817ccf4a065c5d9d7f2cfbe7c1d78c" + }, + "mgcv": { + "Package": "mgcv", + "Version": "1.9-1", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "110ee9d83b496279960e162ac97764ce" + }, + "mime": { + "Package": "mime", + "Version": "0.12", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "18e9c28c1d3ca1560ce30658b22ce104" + }, + "modelr": { + "Package": "modelr", + "Version": "0.1.11", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "4f50122dc256b1b6996a4703fecea821" + }, + "munsell": { + "Package": "munsell", + "Version": "0.5.1", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "4fd8900853b746af55b81fda99da7695" + }, + "nlme": { + "Package": "nlme", + "Version": "3.1-166", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "ccbb8846be320b627e6aa2b4616a2ded" + }, + "openssl": { + "Package": "openssl", + "Version": "2.2.2", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "d413e0fef796c9401a4419485f709ca1" + }, + "openxlsx": { + "Package": "openxlsx", + "Version": "4.2.7.1", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "14304e44a0f90fa2d0f905472333c561" + }, + "pillar": { + "Package": "pillar", + "Version": "1.9.0", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "15da5a8412f317beeee6175fbc76f4bb" + }, + "pkgconfig": { + "Package": "pkgconfig", + "Version": "2.0.3", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "01f28d4278f15c76cddbea05899c5d6f" + }, + "prettyunits": { + "Package": "prettyunits", + "Version": "1.2.0", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "6b01fc98b1e86c4f705ce9dcfd2f57c7" + }, + "processx": { + "Package": "processx", + "Version": "3.8.4", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "0c90a7d71988856bad2a2a45dd871bb9" + }, + "progress": { + "Package": "progress", + "Version": "1.2.3", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "f4625e061cb2865f111b47ff163a5ca6" + }, + "promises": { + "Package": "promises", + "Version": "1.3.0", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "434cd5388a3979e74be5c219bcd6e77d" + }, + "ps": { + "Package": "ps", + "Version": "1.8.0", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "4b9c8485b0c7eecdf0a9ba5132a45576" + }, + "purrr": { + "Package": "purrr", + "Version": "1.0.2", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "1cba04a4e9414bdefc9dcaa99649a8dc" + }, + "ragg": { + "Package": "ragg", + "Version": "1.3.3", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "0595fe5e47357111f29ad19101c7d271" + }, + "rappdirs": { + "Package": "rappdirs", + "Version": "0.3.3", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "5e3c5dc0b071b21fa128676560dbe94d" + }, + "readr": { + "Package": "readr", + "Version": "2.1.5", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "9de96463d2117f6ac49980577939dfb3" + }, + "readxl": { + "Package": "readxl", + "Version": "1.4.3", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "8cf9c239b96df1bbb133b74aef77ad0a" + }, + "rematch": { + "Package": "rematch", + "Version": "2.0.0", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "cbff1b666c6fa6d21202f07e2318d4f1" + }, + "rematch2": { + "Package": "rematch2", + "Version": "2.1.2", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "76c9e04c712a05848ae7a23d2f170a40" + }, + "renv": { + "Package": "renv", + "Version": "1.0.11", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "47623f66b4e80b3b0587bc5d7b309888" + }, + "reprex": { + "Package": "reprex", + "Version": "2.1.1", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "97b1d5361a24d9fb588db7afe3e5bcbf" + }, + "rlang": { + "Package": "rlang", + "Version": "1.1.4", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "3eec01f8b1dee337674b2e34ab1f9bc1" + }, + "rmarkdown": { + "Package": "rmarkdown", + "Version": "2.28", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "062470668513dcda416927085ee9bdc7" + }, + "rstudioapi": { + "Package": "rstudioapi", + "Version": "0.17.0", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "fb9f5fce8f609e9b66f0bea5c783f88a" + }, + "rvest": { + "Package": "rvest", + "Version": "1.0.4", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "0bcf0c6f274e90ea314b812a6d19a519" + }, + "sass": { + "Package": "sass", + "Version": "0.4.9", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "d53dbfddf695303ea4ad66f86e99b95d" + }, + "scales": { + "Package": "scales", + "Version": "1.3.0", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "c19df082ba346b0ffa6f833e92de34d1" + }, + "selectr": { + "Package": "selectr", + "Version": "0.4-2", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "3838071b66e0c566d55cc26bd6e27bf4" + }, + "shiny": { + "Package": "shiny", + "Version": "1.9.1", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "6a293995a66e12c48d13aa1f957d09c7" + }, + "shiny.i18n": { + "Package": "shiny.i18n", + "Version": "0.3.0", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "fb1b47e69750065a4f3c8c4ef24e4891" + }, + "sourcetools": { + "Package": "sourcetools", + "Version": "0.1.7-1", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "5f5a7629f956619d519205ec475fe647" + }, + "stringi": { + "Package": "stringi", + "Version": "1.8.4", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "39e1144fd75428983dc3f63aa53dfa91" + }, + "stringr": { + "Package": "stringr", + "Version": "1.5.1", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "960e2ae9e09656611e0b8214ad543207" + }, + "sys": { + "Package": "sys", + "Version": "3.4.3", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "de342ebfebdbf40477d0758d05426646" + }, + "systemfonts": { + "Package": "systemfonts", + "Version": "1.1.0", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "213b6b8ed5afbf934843e6c3b090d418" + }, + "textshaping": { + "Package": "textshaping", + "Version": "0.4.0", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "5142f8bc78ed3d819d26461b641627ce" + }, + "tibble": { + "Package": "tibble", + "Version": "3.2.1", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "a84e2cc86d07289b3b6f5069df7a004c" + }, + "tidyr": { + "Package": "tidyr", + "Version": "1.3.1", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "915fb7ce036c22a6a33b5a8adb712eb1" + }, + "tidyselect": { + "Package": "tidyselect", + "Version": "1.2.1", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "829f27b9c4919c16b593794a6344d6c0" + }, + "tidyverse": { + "Package": "tidyverse", + "Version": "2.0.0", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "c328568cd14ea89a83bd4ca7f54ae07e" + }, + "timechange": { + "Package": "timechange", + "Version": "0.3.0", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "c5f3c201b931cd6474d17d8700ccb1c8" + }, + "tinytex": { + "Package": "tinytex", + "Version": "0.53", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "9db859e8aabbb474293dde3097839420" + }, + "tzdb": { + "Package": "tzdb", + "Version": "0.4.0", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "f561504ec2897f4d46f0c7657e488ae1" + }, + "utf8": { + "Package": "utf8", + "Version": "1.2.4", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "62b65c52671e6665f803ff02954446e9" + }, + "uuid": { + "Package": "uuid", + "Version": "1.2-1", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "34e965e62a41fcafb1ca60e9b142085b" + }, + "vctrs": { + "Package": "vctrs", + "Version": "0.6.5", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "c03fa420630029418f7e6da3667aac4a" + }, + "viridisLite": { + "Package": "viridisLite", + "Version": "0.4.2", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "c826c7c4241b6fc89ff55aaea3fa7491" + }, + "vroom": { + "Package": "vroom", + "Version": "1.6.5", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "390f9315bc0025be03012054103d227c" + }, + "withr": { + "Package": "withr", + "Version": "3.0.1", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "07909200e8bbe90426fbfeb73e1e27aa" + }, + "xfun": { + "Package": "xfun", + "Version": "0.48", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "89e455b87c84e227eb7f60a1b4e5fe1f" + }, + "xml2": { + "Package": "xml2", + "Version": "1.3.6", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "1d0336142f4cd25d8d23cd3ba7a8fb61" + }, + "xtable": { + "Package": "xtable", + "Version": "1.8-4", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "b8acdf8af494d9ec19ccb2481a9b11c2" + }, + "yaml": { + "Package": "yaml", + "Version": "2.3.10", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "51dab85c6c98e50a18d7551e9d49f76c" + }, + "zip": { + "Package": "zip", + "Version": "2.3.1", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "fcc4bd8e6da2d2011eb64a5e5cc685ab" + } + } } diff --git a/renv/activate.R b/renv/activate.R index 613f836..79c701c 100644 --- a/renv/activate.R +++ b/renv/activate.R @@ -2,89 +2,32 @@ local({ # the requested version of renv - version <- "0.14.0" - attr(version, "sha") <- NULL + version <- "1.0.11" # the project directory - project <- Sys.getenv("RENV_PROJECT") - if (!nzchar(project)) - project <- getwd() + 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) + # allow environment variable to control activation + activate <- Sys.getenv("RENV_ACTIVATE_PROJECT") + if (!nzchar(activate)) { - # 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)) + # don't auto-activate when R CMD INSTALL is running + if (nzchar(Sys.getenv("R_INSTALL_PKG"))) return(FALSE) - # next, check environment variables - # TODO: 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()) - } + } + # bail if activation was explicitly disabled + if (tolower(activate) %in% c("false", "f", "0")) return(FALSE) - } - # avoid recursion - if (identical(getOption("renv.autoloader.running"), TRUE)) { - warning("ignoring recursive attempt to run renv autoloader") + if (nzchar(Sys.getenv("RENV_R_INITIALIZING"))) 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) + Sys.setenv("RENV_R_INITIALIZING" = "true") + on.exit(Sys.unsetenv("RENV_R_INITIALIZING"), add = TRUE) # signal that we've consented to use renv options(renv.consent = TRUE) @@ -93,159 +36,33 @@ local({ # 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()) + # check to see if renv has already been loaded + if ("renv" %in% loadedNamespaces()) { + + # if renv has already been loaded, and it's the requested version of renv, + # nothing to do + spec <- .getNamespaceInfo(.getNamespace("renv"), "spec") + if (identical(spec[["version"]], version)) + return(invisible(TRUE)) + + # otherwise, unload and attempt to load the correct version of renv 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.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 - } - + + # load bootstrap tools 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) + tarball <- tryCatch(renv_bootstrap_download(version), error = identity) + if (inherits(tarball, "error")) + stop("failed to download renv ", version) # 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") + status <- tryCatch(renv_bootstrap_install(version, tarball, library), error = identity) + if (inherits(status, "error")) + stop("failed to install renv ", version) - # add empty line to break up bootstrapping from normal output - catf("") - - return(invisible()) } renv_bootstrap_tests_running <- function() { @@ -254,32 +71,23 @@ 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)) { - - # 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) - + if (!is.na(repos)) 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()) + return(getOption("renv.tests.repos")) # retrieve current repos repos <- getOption("repos") # ensure @CRAN@ entries are resolved - repos[repos == "@CRAN@"] <- cran + repos[repos == "@CRAN@"] <- getOption( + "renv.repos.cran", + "https://cloud.r-project.org" + ) # add in renv.bootstrap.repos if set default <- c(FALLBACK = "https://cloud.r-project.org") @@ -292,60 +100,31 @@ local({ } - 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$Repositories - if (length(repos) == 0) - return(NULL) - - keys <- vapply(repos, `[[`, "Name", FUN.VALUE = character(1)) - vals <- vapply(repos, `[[`, "URL", FUN.VALUE = character(1)) - names(vals) <- keys - - return(vals) - - } - renv_bootstrap_download <- function(version) { - sha <- attr(version, "sha", exact = TRUE) + # if the renv version number has 4 components, assume it must + # be retrieved via github + nv <- numeric_version(version) + components <- unclass(nv)[[1]] - methods <- if (!is.null(sha)) { - - # attempting to bootstrap a development version of renv - c( - function() renv_bootstrap_download_tarball(sha), - function() renv_bootstrap_download_github(sha) + methods <- if (length(components) == 4L) { + list( + renv_bootstrap_download_github ) - } else { - - # attempting to bootstrap a release version of renv - c( - function() renv_bootstrap_download_tarball(version), - function() renv_bootstrap_download_cran_latest(version), - function() renv_bootstrap_download_cran_archive(version) + list( + renv_bootstrap_download_cran_latest, + renv_bootstrap_download_cran_archive ) - } for (method in methods) { - path <- tryCatch(method(), error = identity) + path <- tryCatch(method(version), error = identity) if (is.character(path) && file.exists(path)) return(path) } - stop("All download methods failed") + stop("failed to download renv ", version) } @@ -361,78 +140,43 @@ local({ if (fixup) mode <- "w+b" - args <- list( + utils::download.file( url = url, destfile = destfile, mode = mode, quiet = TRUE ) - if ("headers" %in% names(formals(utils::download.file))) { - headers <- renv_bootstrap_download_custom_headers(url) - if (length(headers) && is.character(headers)) - args$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) + + message("* Downloading renv ", version, " ... ", appendLF = FALSE) + 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), + info <- tryCatch( + utils::download.packages( + pkgs = "renv", + destdir = tempdir(), + repos = repos, + type = type, + quiet = TRUE + ), condition = identity ) - if (inherits(status, "condition")) + if (inherits(info, "condition")) { + message("FAILED") return(FALSE) + } # report success and return - destfile + message("OK (downloaded ", type, ")") + info[1, 2] } @@ -451,21 +195,10 @@ 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( - do.call(utils::available.packages, args), + utils::available.packages(type = type, repos = repos), stringsAsFactors = FALSE ), error = identity @@ -499,6 +232,8 @@ 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( @@ -506,55 +241,18 @@ local({ condition = identity ) - if (identical(status, 0L)) + if (identical(status, 0L)) { + message("OK") return(destfile) + } } + message("FAILED") 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") @@ -562,21 +260,23 @@ local({ return(FALSE) # prepare download options - token <- renv_bootstrap_github_token() - if (nzchar(Sys.which("curl")) && nzchar(token)) { + pat <- Sys.getenv("GITHUB_PAT") + if (nzchar(Sys.which("curl")) && nzchar(pat)) { fmt <- "--location --fail --header \"Authorization: token %s\"" - extra <- sprintf(fmt, token) + extra <- sprintf(fmt, pat) 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)) { + } else if (nzchar(Sys.which("wget")) && nzchar(pat)) { fmt <- "--header=\"Authorization: token %s\"" - extra <- sprintf(fmt, token) + extra <- sprintf(fmt, pat) 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) @@ -586,113 +286,40 @@ local({ condition = identity ) - if (!identical(status, 0L)) + if (!identical(status, 0L)) { + message("FAILED") 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) + message("OK") + return(destfile) - 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", "-l", shQuote(library), shQuote(tarball)) + output <- system2(r, args, stdout = TRUE, stderr = TRUE) + message("Done!") - args <- c( - "--vanilla", "CMD", "INSTALL", "--no-multiarch", - "-l", shQuote(path.expand(library)), - shQuote(path.expand(tarball)) - ) + # 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()) + } - system2(R, args, stdout = TRUE, stderr = TRUE) + status } @@ -733,9 +360,6 @@ 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()) @@ -875,91 +499,49 @@ local({ 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 = "/")) + return(path) - path <- renv_bootstrap_library_root_impl(project) - if (!is.null(path)) { + path <- Sys.getenv("RENV_PATHS_LIBRARY_ROOT", unset = NA) + if (!is.na(path)) { name <- renv_bootstrap_library_root_name(project) - return(paste(c(path, prefix, name), collapse = "/")) + return(file.path(path, name)) } - 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")) - } + prefix <- renv_bootstrap_profile_prefix() + paste(c(project, prefix, "renv/library"), collapse = "/") } - 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") + renv_bootstrap_validate_version <- function(version) { - # 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) + loadedversion <- utils::packageDescription("renv", fields = "Version") + if (version == loadedversion) 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 = "@") + # 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 = "@") else - paste("renv", description[["Version"]], sep = "@") + paste("renv", loadedversion, sep = "@") - # display both loaded version + sha if available - friendly <- renv_bootstrap_version_friendly( - version = description[["Version"]], - sha = if (dev) description[["RemoteSha"]] + 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" ) - 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) + msg <- sprintf(fmt, loadedversion, version, remote) + warning(msg, call. = FALSE) 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-") @@ -979,12 +561,6 @@ local({ # 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) @@ -1000,7 +576,7 @@ local({ 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) + path <- file.path(project, "renv/local/profile") if (!file.exists(path)) return(NULL) @@ -1011,7 +587,7 @@ local({ # set RENV_PROFILE profile <- contents[[1L]] - if (!profile %in% c("", "default")) + if (nzchar(profile)) Sys.setenv(RENV_PROFILE = profile) profile @@ -1021,7 +597,7 @@ local({ renv_bootstrap_profile_prefix <- function() { profile <- renv_bootstrap_profile_get() if (!is.null(profile)) - return(file.path("profiles", profile, "renv")) + return(file.path("renv/profiles", profile)) } renv_bootstrap_profile_get <- function() { @@ -1045,245 +621,6 @@ local({ 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(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) { - - 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_default <- function(file = NULL, text = NULL) { - - # find strings in the JSON - text <- paste(text %||% readLines(file, warn = FALSE), collapse = "\n") - pattern <- '["](?:(?:\\\\.)|(?:[^"\\\\]))*?["]' - locs <- gregexpr(pattern, text, perl = TRUE)[[1]] - - # if any are found, replace them with placeholders - replaced <- text - strings <- character() - replacements <- character() - - if (!identical(c(locs), -1L)) { - - # get the string values - starts <- locs - ends <- locs + attr(locs, "match.length") - 1L - strings <- substring(text, starts, ends) - - # only keep those requiring escaping - strings <- grep("[[\\]{}:]", strings, perl = TRUE, value = TRUE) - - # compute replacements - replacements <- sprintf('"\032%i\032"', seq_along(strings)) - - # replace the strings - mapply(function(string, replacement) { - replaced <<- sub(string, replacement, replaced, fixed = TRUE) - }, strings, replacements) - - } - - # transform the JSON into something the R parser understands - transformed <- replaced - transformed <- gsub("{}", "`names<-`(list(), character())", transformed, fixed = TRUE) - transformed <- gsub("[[{]", "list(", transformed, perl = TRUE) - transformed <- gsub("[]}]", ")", transformed, perl = TRUE) - transformed <- gsub(":", "=", transformed, fixed = TRUE) - text <- paste(transformed, collapse = "\n") - - # parse it - json <- parse(text = text, keep.source = FALSE, srcfile = NULL)[[1L]] - - # construct map between source strings, replaced strings - map <- as.character(parse(text = strings)) - names(map) <- as.character(parse(text = replacements)) - - # convert to list - map <- as.list(map) - - # remap strings in object - remapped <- renv_json_read_remap(json, map) - - # evaluate - eval(remapped, envir = baseenv()) - - } - - renv_json_read_remap <- function(json, map) { - - # fix names - if (!is.null(names(json))) { - lhs <- match(names(json), names(map), nomatch = 0L) - rhs <- match(names(map), names(json), nomatch = 0L) - names(json)[rhs] <- map[lhs] - } - - # fix values - if (is.character(json)) - return(map[[json]] %||% json) - - # handle true, false, null - if (is.name(json)) { - text <- as.character(json) - if (text == "true") - return(TRUE) - else if (text == "false") - return(FALSE) - else if (text == "null") - return(NULL) - } - - # recurse - if (is.recursive(json)) { - for (i in seq_along(json)) { - json[i] <- list(renv_json_read_remap(json[[i]], map)) - } - } - - json - - } # load the renv profile, if any renv_bootstrap_profile_load(project) @@ -1297,9 +634,35 @@ local({ # construct full libpath libpath <- file.path(root, prefix) - # run bootstrap code - renv_bootstrap_exec(project, libpath, version) + # 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." + ) - invisible() + warning(paste(msg, collapse = "\n"), call. = FALSE) }) diff --git a/renv/settings.json b/renv/settings.json new file mode 100644 index 0000000..f836f3f --- /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": [], + "snapshot.type": "implicit", + "use.cache": true, + "vcs.ignore.cellar": true, + "vcs.ignore.library": true, + "vcs.ignore.local": true, + "vcs.manage.ignores": true +}