diff --git a/renv.lock b/renv.lock index 41b7465..3786297 100644 --- a/renv.lock +++ b/renv.lock @@ -1,6 +1,6 @@ { "R": { - "Version": "4.2.1", + "Version": "4.3.0", "Repositories": [ { "Name": "CRAN", @@ -11,7 +11,7 @@ "Packages": { "MASS": { "Package": "MASS", - "Version": "7.3-58.3", + "Version": "7.3-60", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -22,15 +22,16 @@ "stats", "utils" ], - "Hash": "9586b552d57f5516fe4d25398c1bacd6" + "Hash": "a56a6365b3fa73293ea8d084be0d9bb0" }, "Matrix": { "Package": "Matrix", - "Version": "1.5-3", + "Version": "1.6-1.1", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R", + "grDevices", "graphics", "grid", "lattice", @@ -38,7 +39,7 @@ "stats", "utils" ], - "Hash": "4006dffe49958d2dd591c17e61e60591" + "Hash": "1a00d4828f33a9d690806e98bd17150c" }, "R6": { "Package": "R6", @@ -62,24 +63,24 @@ }, "Rcpp": { "Package": "Rcpp", - "Version": "1.0.10", + "Version": "1.0.11", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "methods", "utils" ], - "Hash": "e749cae40fa9ef469b6050959517453c" + "Hash": "ae6cbbe1492f4de79c45fce06f967ce8" }, "askpass": { "Package": "askpass", - "Version": "1.1", + "Version": "1.2.0", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "sys" ], - "Hash": "e8a22846fff485f0be3770c2da758713" + "Hash": "cad6cf7f1d5f6e906700b9d3e718c796" }, "base64enc": { "Package": "base64enc", @@ -117,7 +118,7 @@ }, "bslib": { "Package": "bslib", - "Version": "0.4.2", + "Version": "0.5.1", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -133,18 +134,18 @@ "rlang", "sass" ], - "Hash": "a7fbf03946ad741129dc81098722fca1" + "Hash": "283015ddfbb9d7bf15ea9f0b5698f0d9" }, "cachem": { "Package": "cachem", - "Version": "1.0.7", + "Version": "1.0.8", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "fastmap", "rlang" ], - "Hash": "cda74447c42f529de601fe4d4050daef" + "Hash": "c35768291560ce302c0a6589f92e837d" }, "callr": { "Package": "callr", @@ -196,7 +197,7 @@ }, "colourpicker": { "Package": "colourpicker", - "Version": "1.2.0", + "Version": "1.3.0", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -210,7 +211,7 @@ "shinyjs", "utils" ], - "Hash": "ca4d99d106687d68392ffe270081bfc0" + "Hash": "daec8f7d4ba89df06fe2c0802c3a9dac" }, "commonmark": { "Package": "commonmark", @@ -219,32 +220,15 @@ "Repository": "CRAN", "Hash": "d691c61bff84bd63c383874d2d0c3307" }, - "covr": { - "Package": "covr", - "Version": "3.6.1", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "crayon", - "digest", - "httr", - "jsonlite", - "methods", - "rex", - "stats", - "utils", - "withr", - "yaml" - ], - "Hash": "a861cee34fbb4b107a73dd414ef56724" - }, "cpp11": { "Package": "cpp11", - "Version": "0.4.3", + "Version": "0.4.6", "Source": "Repository", "Repository": "CRAN", - "Hash": "ed588261931ee3be2c700d22e94a29ab" + "Requirements": [ + "R" + ], + "Hash": "707fae4bbf73697ec8d85f9d7076c061" }, "crayon": { "Package": "crayon", @@ -260,7 +244,7 @@ }, "credentials": { "Package": "credentials", - "Version": "1.3.2", + "Version": "2.0.1", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -270,17 +254,17 @@ "openssl", "sys" ], - "Hash": "93762d0a34d78e6a025efdbfb5c6bb41" + "Hash": "c7844b32098dcbd1c59cbd8dddb4ecc6" }, "curl": { "Package": "curl", - "Version": "5.0.0", + "Version": "5.1.0", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R" ], - "Hash": "e4f97056611e8e6b8b852d13b7400cf1" + "Hash": "9123f3ef96a2c1a93927d828b2fe7d4c" }, "desc": { "Package": "desc", @@ -313,18 +297,18 @@ }, "digest": { "Package": "digest", - "Version": "0.6.31", + "Version": "0.6.33", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R", "utils" ], - "Hash": "8b708f296afd9ae69f450f9640be8990" + "Hash": "b18a9cf3c003977b0cc49d5e76ebe48d" }, "downlit": { "Package": "downlit", - "Version": "0.4.2", + "Version": "0.4.3", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -340,7 +324,7 @@ "withr", "yaml" ], - "Hash": "79bf3f66590752ffbba20f8d2da94c7c" + "Hash": "14fa1f248b60ed67e1f5418391a17b14" }, "ellipsis": { "Package": "ellipsis", @@ -355,18 +339,18 @@ }, "evaluate": { "Package": "evaluate", - "Version": "0.20", + "Version": "0.22", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R", "methods" ], - "Hash": "4b68aa51edd89a0e044a66e75ae3cc6c" + "Hash": "66f39c7a21e03c4dcb2c2d21d738d603" }, "fansi": { "Package": "fansi", - "Version": "1.0.4", + "Version": "1.0.5", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -374,7 +358,7 @@ "grDevices", "utils" ], - "Hash": "1d9e7ad3c8312a192dea7d3db0274fde" + "Hash": "3e8583a60163b4bc1a80016e63b9959e" }, "farver": { "Package": "farver", @@ -392,7 +376,7 @@ }, "fontawesome": { "Package": "fontawesome", - "Version": "0.5.0", + "Version": "0.5.2", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -400,22 +384,22 @@ "htmltools", "rlang" ], - "Hash": "e80750aec5717dedc019ad7ee40e4a7c" + "Hash": "c2efdd5f0bcd1ea861c2d4e2a883a67d" }, "fs": { "Package": "fs", - "Version": "1.6.1", + "Version": "1.6.3", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R", "methods" ], - "Hash": "f4dcd23b67e33d851d2079f703e8b985" + "Hash": "47b5f30c720c23999b913a1a635cf0bb" }, "gert": { "Package": "gert", - "Version": "1.9.2", + "Version": "2.0.0", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -426,24 +410,26 @@ "sys", "zip" ], - "Hash": "9122b3958e749badb5c939f498038b57" + "Hash": "bbbd21a253d473f4671d7dcbd6d8971f" }, "ggfun": { "Package": "ggfun", - "Version": "0.0.9", + "Version": "0.1.3", "Source": "Repository", "Repository": "CRAN", "Requirements": [ + "R", + "cli", "ggplot2", "grid", "rlang", "utils" ], - "Hash": "c970ab268b09d3c8b0f524294050860f" + "Hash": "4657d320971a330ecffd0e1260f58214" }, "ggimage": { "Package": "ggimage", - "Version": "0.3.1", + "Version": "0.3.3", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -458,13 +444,14 @@ "scales", "tibble", "tools", - "utils" + "utils", + "withr" ], - "Hash": "a7919e11761293f25eeb1562d3e4342a" + "Hash": "18c57347f13a654ef8683a6676042624" }, "ggplot2": { "Package": "ggplot2", - "Version": "3.4.1", + "Version": "3.4.4", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -485,11 +472,11 @@ "vctrs", "withr" ], - "Hash": "d494daf77c4aa7f084dbbe6ca5dcaca7" + "Hash": "313d31eff2274ecf4c1d3581db7241f9" }, "ggplotify": { "Package": "ggplotify", - "Version": "0.1.0", + "Version": "0.1.2", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -501,7 +488,7 @@ "gridGraphics", "yulab.utils" ], - "Hash": "acbcedf783cdb8710168aa0edba42ac0" + "Hash": "1547863db3b472cf7181973acf649f1a" }, "gh": { "Package": "gh", @@ -554,7 +541,7 @@ }, "gtable": { "Package": "gtable", - "Version": "0.3.3", + "Version": "0.3.4", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -565,7 +552,7 @@ "lifecycle", "rlang" ], - "Hash": "b44addadb528a0d227794121c00572a0" + "Hash": "b29cf3031f49b04ab9c852c912547eef" }, "hexSticker": { "Package": "hexSticker", @@ -614,7 +601,7 @@ }, "htmltools": { "Package": "htmltools", - "Version": "0.5.5", + "Version": "0.5.6.1", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -627,7 +614,7 @@ "rlang", "utils" ], - "Hash": "ba0240784ad50a62165058a27459304a" + "Hash": "1e12fe667316a76508898839ecfb2d00" }, "htmlwidgets": { "Package": "htmlwidgets", @@ -646,7 +633,7 @@ }, "httpuv": { "Package": "httpuv", - "Version": "1.6.9", + "Version": "1.6.12", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -657,11 +644,11 @@ "promises", "utils" ], - "Hash": "1046aa31a57eae8b357267a56a0b6d8b" + "Hash": "c992f75861325961c29a188b45e549f7" }, "httr": { "Package": "httr", - "Version": "1.4.5", + "Version": "1.4.7", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -672,11 +659,11 @@ "mime", "openssl" ], - "Hash": "f6844033201269bec3ca0097bc6c97b3" + "Hash": "ac107251d9d9fd72f0ca8049988f1d7f" }, "httr2": { "Package": "httr2", - "Version": "0.2.2", + "Version": "0.2.3", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -691,7 +678,7 @@ "rlang", "withr" ], - "Hash": "5c09fe33064978ede54de42309c8b532" + "Hash": "193bb297368afbbb42dc85784a46b36e" }, "ini": { "Package": "ini", @@ -723,17 +710,17 @@ }, "jsonlite": { "Package": "jsonlite", - "Version": "1.8.4", + "Version": "1.8.7", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "methods" ], - 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"Hash": "b64cdbb2b340437c4ee047a1f4c4377b" - }, - "lazyeval": { - "Package": "lazyeval", - "Version": "0.2.2", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R" - ], - "Hash": "d908914ae53b04d4c0c0fd72ecc35370" + "Hash": "7c5e89f04e72d6611c77451f6331a091" }, "lifecycle": { "Package": "lifecycle", @@ -809,7 +786,7 @@ }, "magick": { "Package": "magick", - "Version": "2.7.4", + "Version": "2.8.1", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -817,7 +794,7 @@ "curl", "magrittr" ], - "Hash": "92dd08195d2270e188dcac8d4b219e84" + "Hash": "691d5b9fd0e7ee9b56301fc8735a2e1f" }, "magrittr": { "Package": "magrittr", @@ -842,7 +819,7 @@ }, "mgcv": { "Package": "mgcv", - "Version": "1.8-42", + "Version": "1.9-0", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -855,7 +832,7 @@ "stats", "utils" ], - "Hash": "3460beba7ccc8946249ba35327ba902a" + "Hash": "086028ca0460d0c368028d3bda58f31b" }, "mime": { "Package": "mime", @@ -892,7 +869,7 @@ }, "nlme": { "Package": "nlme", - "Version": "3.1-162", + "Version": "3.1-163", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -902,17 +879,17 @@ "stats", "utils" ], - "Hash": "0984ce8da8da9ead8643c5cbbb60f83e" + "Hash": "8d1938040a05566f4f7a14af4feadd6b" }, "openssl": { "Package": "openssl", - "Version": "2.0.6", + "Version": "2.1.1", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "askpass" ], - "Hash": "0f7cd2962e3044bb940cca4f4b5cecbe" + "Hash": "2a0dc8c6adfb6f032e4d4af82d258ab5" }, "pillar": { "Package": "pillar", @@ -931,6 +908,24 @@ ], "Hash": "15da5a8412f317beeee6175fbc76f4bb" }, + "pkgbuild": { + "Package": "pkgbuild", + "Version": "1.4.2", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "R", + "R6", + "callr", + "cli", + "crayon", + "desc", + "prettyunits", + "processx", + "rprojroot" + ], + "Hash": "beb25b32a957a22a5c301a9e441190b3" + }, "pkgconfig": { "Package": "pkgconfig", "Version": "2.0.3", @@ -973,7 +968,7 @@ }, "pkgload": { "Package": "pkgload", - "Version": "1.3.2", + "Version": "1.3.3", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -984,12 +979,13 @@ "fs", "glue", "methods", + "pkgbuild", "rlang", "rprojroot", "utils", "withr" ], - "Hash": "6b0c222c5071efe0f3baf3dae9aa40e2" + "Hash": "903d68319ae9923fb2e2ee7fa8230b91" }, "praise": { "Package": "praise", @@ -998,9 +994,19 @@ "Repository": "CRAN", "Hash": "a555924add98c99d2f411e37e7d25e9f" }, + "prettyunits": { + "Package": "prettyunits", + "Version": "1.2.0", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "R" + ], + "Hash": "6b01fc98b1e86c4f705ce9dcfd2f57c7" + }, "processx": { "Package": "processx", - "Version": "3.8.0", + "Version": "3.8.2", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -1009,37 +1015,38 @@ "ps", "utils" ], - "Hash": "a33ee2d9bf07564efb888ad98410da84" + "Hash": "3efbd8ac1be0296a46c55387aeace0f3" }, "promises": { "Package": "promises", - "Version": "1.2.0.1", + "Version": "1.2.1", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R6", "Rcpp", + "fastmap", "later", "magrittr", "rlang", "stats" ], - "Hash": "4ab2c43adb4d4699cf3690acd378d75d" + "Hash": "0d8a15c9d000970ada1ab21405387dee" }, "ps": { "Package": "ps", - "Version": "1.7.3", + "Version": "1.7.5", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R", "utils" ], - "Hash": "ebaacc87f539b1100e285e9e5d6496ad" + "Hash": "709d852d33178db54b17c722e5b1e594" }, "purrr": { "Package": "purrr", - "Version": "1.0.1", + "Version": "1.0.2", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -1050,18 +1057,18 @@ "rlang", "vctrs" ], - "Hash": "d71c815267c640f17ddbf7f16144b4bb" + "Hash": "1cba04a4e9414bdefc9dcaa99649a8dc" }, "ragg": { "Package": "ragg", - "Version": "1.2.5", + "Version": "1.2.6", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "systemfonts", "textshaping" ], - "Hash": "690bc058ea2b1b8a407d3cfe3dce3ef9" + "Hash": "6ba2fa8740abdc2cc148407836509901" }, "rappdirs": { "Package": "rappdirs", @@ -1085,23 +1092,13 @@ }, "renv": { "Package": "renv", - "Version": "0.17.2", + "Version": "1.0.3", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "utils" ], - "Hash": "aaf3c7f769695266a2113db67a25148b" - }, - "rex": { - "Package": "rex", - "Version": "1.2.1", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "lazyeval" - ], - "Hash": "ae34cd56890607370665bee5bd17812f" + "Hash": "41b847654f567341725473431dd0d5ab" }, "rjson": { "Package": "rjson", @@ -1115,24 +1112,25 @@ }, "rlang": { "Package": "rlang", - "Version": "1.1.0", + "Version": "1.1.1", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R", "utils" ], - "Hash": "dc079ccd156cde8647360f473c1fa718" + "Hash": "a85c767b55f0bf9b7ad16c6d7baee5bb" }, "rmarkdown": { "Package": "rmarkdown", - "Version": "2.20", + "Version": "2.25", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R", "bslib", "evaluate", + "fontawesome", "htmltools", "jquerylib", "jsonlite", @@ -1145,7 +1143,7 @@ "xfun", "yaml" ], - "Hash": "716fde5382293cc94a71f68c85b78d19" + "Hash": "d65e35823c817f09f4de424fcdfa812a" }, "rprojroot": { "Package": "rprojroot", @@ -1159,14 +1157,14 @@ }, "rstudioapi": { "Package": "rstudioapi", - "Version": "0.14", + "Version": "0.15.0", "Source": "Repository", "Repository": "CRAN", - "Hash": "690bd2acc42a9166ce34845884459320" + "Hash": "5564500e25cffad9e22244ced1379887" }, "sass": { "Package": "sass", - "Version": "0.4.5", + "Version": "0.4.7", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -1176,7 +1174,7 @@ "rappdirs", "rlang" ], - "Hash": "2bb4371a4c80115518261866eab6ab11" + "Hash": "6bd4d33b50ff927191ec9acbf52fd056" }, "scales": { "Package": "scales", @@ -1198,7 +1196,7 @@ }, "shiny": { "Package": "shiny", - "Version": "1.7.4", + "Version": "1.7.5.1", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -1228,7 +1226,7 @@ "withr", "xtable" ], - "Hash": "c2eae3d8c670fa9dfa35a12066f4a1d5" + "Hash": "5ec01cc255f2138fc2f0dc74d2b1a1a1" }, "shinyjs": { "Package": "shinyjs", @@ -1245,7 +1243,7 @@ }, "showtext": { "Package": "showtext", - "Version": "0.9-5", + "Version": "0.9-6", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -1253,7 +1251,7 @@ "showtextdb", "sysfonts" ], - "Hash": "b588dee88e238bf811e27f12edee9433" + "Hash": "c0fd332d248b195bbcb94a0dfda37b0d" }, "showtextdb": { "Package": "showtextdb", @@ -1308,10 +1306,10 @@ }, "sys": { "Package": "sys", - "Version": "3.4.1", + "Version": "3.4.2", "Source": "Repository", "Repository": "CRAN", - "Hash": "34c16f1ef796057bfa06d3f4ff818a5d" + "Hash": "3a1be13d68d47a8cd0bfd74739ca1555" }, "sysfonts": { "Package": "sysfonts", @@ -1322,18 +1320,18 @@ }, "systemfonts": { "Package": "systemfonts", - "Version": "1.0.4", + "Version": "1.0.5", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R", "cpp11" ], - "Hash": "90b28393209827327de889f49935140a" + "Hash": "15b594369e70b975ba9f064295983499" }, "testthat": { "Package": "testthat", - "Version": "3.1.7", + "Version": "3.2.0", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -1359,11 +1357,11 @@ "waldo", "withr" ], - "Hash": "7eb5fd202a61d2fb78af5869b6c08998" + "Hash": "877508719fcb8c9525eccdadf07a5102" }, "textshaping": { "Package": "textshaping", - "Version": "0.3.6", + "Version": "0.3.7", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -1371,7 +1369,7 @@ "cpp11", "systemfonts" ], - "Hash": "1ab6223d3670fac7143202cb6a2d43d5" + "Hash": "997aac9ad649e0ef3b97f96cddd5622b" }, "tibble": { "Package": "tibble", @@ -1394,17 +1392,17 @@ }, "tinytex": { "Package": "tinytex", - "Version": "0.44", + "Version": "0.48", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "xfun" ], - "Hash": "c0f007e2eeed7722ce13d42b84a22e07" + "Hash": "8f96d229b7311beb32b94cf413b13f84" }, "usethis": { "Package": "usethis", - "Version": "2.1.6", + "Version": "2.2.2", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -1431,21 +1429,21 @@ "withr", "yaml" ], - "Hash": "a67a22c201832b12c036cc059f1d137d" + "Hash": "60e51f0b94d0324dc19e44110098fa9f" }, "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": "0.6.1", + "Version": "0.6.4", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -1455,21 +1453,21 @@ "lifecycle", "rlang" ], - "Hash": "06eceb3a5d716fd0654cc23ca3d71a99" + "Hash": "266c1ca411266ba8f365fcc726444b87" }, "viridisLite": { "Package": "viridisLite", - "Version": "0.4.1", + "Version": "0.4.2", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R" ], - "Hash": "62f4b5da3e08d8e5bcba6cac15603f70" + "Hash": "c826c7c4241b6fc89ff55aaea3fa7491" }, "waldo": { "Package": "waldo", - "Version": "0.4.0", + "Version": "0.5.1", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -1482,7 +1480,7 @@ "rlang", "tibble" ], - "Hash": "035fba89d0c86e2113120f93301b98ad" + "Hash": "2c993415154cdb94649d99ae138ff5e5" }, "whisker": { "Package": "whisker", @@ -1493,7 +1491,7 @@ }, "withr": { "Package": "withr", - "Version": "2.5.0", + "Version": "2.5.1", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -1502,29 +1500,29 @@ "graphics", "stats" ], - "Hash": "c0e49a9760983e81e55cdd9be92e7182" + "Hash": "d77c6f74be05c33164e33fbc85540cae" }, "xfun": { "Package": "xfun", - "Version": "0.38", + "Version": "0.40", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "stats", "tools" ], - "Hash": "1ed71215d45e85562d3b1b29a068ccec" + "Hash": "be07d23211245fc7d4209f54c4e4ffc8" }, "xml2": { "Package": "xml2", - "Version": "1.3.3", + "Version": "1.3.5", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R", "methods" ], - "Hash": "40682ed6a969ea5abfd351eb67833adc" + "Hash": "6c40e5cfcc6aefd88110666e18c31f40" }, "xtable": { "Package": "xtable", @@ -1547,21 +1545,27 @@ }, "yulab.utils": { "Package": "yulab.utils", - "Version": "0.0.6", + "Version": "0.1.0", "Source": "Repository", "Repository": "CRAN", "Requirements": [ + "cli", + "digest", + "fs", + "memoise", + "rlang", "stats", + "tools", "utils" ], - "Hash": "0d0b7cc6da5efc21f07f6b8d966a9cc1" + "Hash": "792b3c5bc98f04a7d49cbd8c55fe0770" }, "zip": { "Package": "zip", - "Version": "2.2.2", + "Version": "2.3.0", "Source": "Repository", "Repository": "CRAN", - "Hash": "c42bfcec3fa6a0cce17ce1f8bc684f88" + "Hash": "d98c94dacb7e0efcf83b0a133a705504" } } } diff --git a/renv/activate.R b/renv/activate.R index e17d588..cb5401f 100644 --- a/renv/activate.R +++ b/renv/activate.R @@ -2,11 +2,27 @@ local({ # the requested version of renv - version <- "0.17.2" + version <- "1.0.3" + attr(version, "sha") <- NULL # the project directory 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({ @@ -60,21 +76,75 @@ local({ # load bootstrap tools `%||%` <- 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) + + } + + 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 +153,32 @@ 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 +217,34 @@ 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") } @@ -236,8 +308,6 @@ 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 +324,10 @@ local({ condition = identity ) - if (inherits(status, "condition")) { - message("FAILED") + if (inherits(status, "condition")) return(FALSE) - } # report success and return - message("OK (downloaded ", type, ")") destfile } @@ -317,8 +384,6 @@ 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 +391,11 @@ local({ condition = identity ) - if (identical(status, 0L)) { - message("OK") + if (identical(status, 0L)) return(destfile) - } } - message("FAILED") return(FALSE) } @@ -356,7 +418,7 @@ 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) @@ -365,10 +427,7 @@ local({ } - fmt <- "* Bootstrapping with tarball at path '%s'." - msg <- sprintf(fmt, tarball) - message(msg) - + catf("- Using local tarball '%s'.", tarball) tarball } @@ -395,8 +454,6 @@ local({ 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 +463,105 @@ 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 +569,7 @@ 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) } @@ -655,34 +779,62 @@ local({ } - renv_bootstrap_validate_version <- function(version) { + renv_bootstrap_validate_version <- function(version, description = NULL) { - loadedversion <- utils::packageDescription("renv", fields = "Version") - if (version == loadedversion) - return(TRUE) + # 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") - # 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 = "@") + # 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 - paste("renv", loadedversion, sep = "@") + renv_bootstrap_validate_version_release(version, description) + + if (valid) + return(TRUE) + + # the loaded version of renv doesn't match the requested version; + # give the user instructions on how to proceed + remote <- if (!is.null(description[["RemoteSha"]])) { + paste("rstudio/renv", description[["RemoteSha"]], sep = "@") + } else { + paste("renv", description[["Version"]], sep = "@") + } + + # display both loaded version + sha if available + friendly <- renv_bootstrap_version_friendly( + version = description[["Version"]], + sha = 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$s into the project library.", + "- Use `renv::record(\"%3$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" ) - - msg <- sprintf(fmt, loadedversion, version, remote) - warning(msg, call. = FALSE) + 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 +858,7 @@ 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 +999,40 @@ 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) { @@ -986,35 +1172,9 @@ 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() })