mirror of
https://github.com/FlipsideCrypto/RMarkdown-template.git
synced 2026-02-06 10:56:44 +00:00
+ URL in header & RENV
This commit is contained in:
Carlos R. Mercado
parent
868328521c
commit
72afc37ee2
1
.gitignore
vendored
1
.gitignore
vendored
@ -47,3 +47,4 @@ po/*~
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# RStudio Connect folder
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rsconnect/
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template.html
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@ -1,3 +1,3 @@
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<head>
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<img src="FLIPSIDE-BRAND-1-WHITE.png">
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<a href="https://science.flipsidecrypto.xyz/research"><img src="FLIPSIDE-BRAND-1-WHITE.png"></a>
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</head>
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353
renv.lock
Normal file
353
renv.lock
Normal file
@ -0,0 +1,353 @@
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{
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"R": {
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"Version": "4.2.1",
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"Repositories": [
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{
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"Name": "CRAN",
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"URL": "https://cran.rstudio.com"
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}
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]
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},
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"Packages": {
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"R6": {
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"Package": "R6",
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"Version": "2.5.1",
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"Source": "Repository",
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"Repository": "CRAN",
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"Hash": "470851b6d5d0ac559e9d01bb352b4021",
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"Requirements": []
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},
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"askpass": {
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"Package": "askpass",
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"Version": "1.1",
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"Source": "Repository",
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"Repository": "CRAN",
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"Hash": "e8a22846fff485f0be3770c2da758713",
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"Requirements": [
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"sys"
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]
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},
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"base64enc": {
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"Package": "base64enc",
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"Version": "0.1-3",
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"Source": "Repository",
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"Repository": "CRAN",
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"Hash": "543776ae6848fde2f48ff3816d0628bc",
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"Requirements": []
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},
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"bslib": {
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"Package": "bslib",
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"Version": "0.4.0",
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"Source": "Repository",
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"Repository": "CRAN",
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"Hash": "be5ee090716ce1671be6cd5d7c34d091",
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"Requirements": [
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"cachem",
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"htmltools",
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"jquerylib",
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"jsonlite",
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"memoise",
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"rlang",
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"sass"
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]
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},
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"cachem": {
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"Package": "cachem",
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"Version": "1.0.6",
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"Source": "Repository",
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"Repository": "CRAN",
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"Hash": "648c5b3d71e6a37e3043617489a0a0e9",
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"Requirements": [
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"fastmap",
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"rlang"
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]
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},
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"curl": {
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"Package": "curl",
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"Version": "4.3.2",
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"Source": "Repository",
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"Repository": "CRAN",
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"Hash": "022c42d49c28e95d69ca60446dbabf88",
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"Requirements": []
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},
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"digest": {
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"Package": "digest",
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"Version": "0.6.29",
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"Source": "Repository",
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"Repository": "CRAN",
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"Hash": "cf6b206a045a684728c3267ef7596190",
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"Requirements": []
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},
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"ellipsis": {
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"Package": "ellipsis",
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"Version": "0.3.2",
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"Source": "Repository",
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"Repository": "CRAN",
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"Hash": "bb0eec2fe32e88d9e2836c2f73ea2077",
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"Requirements": [
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"rlang"
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]
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},
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"evaluate": {
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"Package": "evaluate",
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"Version": "0.15",
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"Source": "Repository",
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"Repository": "CRAN",
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"Hash": "699a7a93d08c962d9f8950b2d7a227f1",
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"Requirements": []
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},
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"fastmap": {
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"Package": "fastmap",
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"Version": "1.1.0",
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"Source": "Repository",
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"Repository": "CRAN",
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"Hash": "77bd60a6157420d4ffa93b27cf6a58b8",
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"Requirements": []
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},
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"fs": {
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"Package": "fs",
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"Version": "1.5.2",
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"Source": "Repository",
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"Repository": "CRAN",
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"Hash": "7c89603d81793f0d5486d91ab1fc6f1d",
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"Requirements": []
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},
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"glue": {
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"Package": "glue",
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"Version": "1.6.2",
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"Source": "Repository",
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"Repository": "CRAN",
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"Hash": "4f2596dfb05dac67b9dc558e5c6fba2e",
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"Requirements": []
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},
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"highr": {
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"Package": "highr",
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"Version": "0.9",
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"Source": "Repository",
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"Repository": "CRAN",
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"Hash": "8eb36c8125038e648e5d111c0d7b2ed4",
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"Requirements": [
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"xfun"
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]
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},
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"htmltools": {
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"Package": "htmltools",
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"Version": "0.5.4",
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"Source": "Repository",
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"Repository": "CRAN",
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"Hash": "9d27e99cc90bd701c0a7a63e5923f9b7",
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"Requirements": [
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"base64enc",
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"digest",
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"ellipsis",
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"fastmap",
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"rlang"
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]
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},
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"httr": {
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"Package": "httr",
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"Version": "1.4.3",
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"Source": "Repository",
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"Repository": "CRAN",
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"Hash": "88d1b310583777edf01ccd1216fb0b2b",
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"Requirements": [
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"R6",
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"curl",
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"jsonlite",
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"mime",
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"openssl"
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]
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},
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"jquerylib": {
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"Package": "jquerylib",
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"Version": "0.1.4",
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"Source": "Repository",
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"Repository": "CRAN",
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"Hash": "5aab57a3bd297eee1c1d862735972182",
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"Requirements": [
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"htmltools"
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]
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},
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"jsonlite": {
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"Package": "jsonlite",
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"Version": "1.8.0",
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"Source": "Repository",
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"Repository": "CRAN",
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"Hash": "d07e729b27b372429d42d24d503613a0",
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"Requirements": []
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},
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"knitr": {
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"Package": "knitr",
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"Version": "1.39",
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"Source": "Repository",
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"Repository": "CRAN",
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"Hash": "029ab7c4badd3cf8af69016b2ba27493",
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"Requirements": [
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"evaluate",
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"highr",
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"stringr",
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"xfun",
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"yaml"
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]
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},
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"magrittr": {
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"Package": "magrittr",
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"Version": "2.0.3",
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"Source": "Repository",
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"Repository": "CRAN",
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"Hash": "7ce2733a9826b3aeb1775d56fd305472",
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"Requirements": []
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},
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"memoise": {
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"Package": "memoise",
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"Version": "2.0.1",
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"Source": "Repository",
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"Repository": "CRAN",
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"Hash": "e2817ccf4a065c5d9d7f2cfbe7c1d78c",
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"Requirements": [
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"cachem",
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"rlang"
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]
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},
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"mime": {
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"Package": "mime",
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"Version": "0.12",
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"Source": "Repository",
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"Repository": "CRAN",
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"Hash": "18e9c28c1d3ca1560ce30658b22ce104",
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"Requirements": []
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},
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"openssl": {
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"Package": "openssl",
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"Version": "2.0.2",
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"Source": "Repository",
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"Repository": "CRAN",
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"Hash": "6d3bef2e305f55c705c674653c7d7d3d",
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"Requirements": [
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"askpass"
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]
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},
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"rappdirs": {
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"Package": "rappdirs",
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"Version": "0.3.3",
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"Source": "Repository",
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"Repository": "CRAN",
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"Hash": "5e3c5dc0b071b21fa128676560dbe94d",
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"Requirements": []
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},
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"renv": {
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"Package": "renv",
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"Version": "0.15.5",
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"Source": "Repository",
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"Repository": "CRAN",
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"Hash": "6a38294e7d12f5d8e656b08c5bd8ae34",
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"Requirements": []
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},
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"rlang": {
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"Package": "rlang",
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"Version": "1.0.4",
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"Source": "Repository",
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"Repository": "CRAN",
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"Hash": "6539dd8c651e67e3b55b5ffea106362b",
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"Requirements": []
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},
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"rmarkdown": {
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"Package": "rmarkdown",
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"Version": "2.17",
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"Source": "Repository",
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"Repository": "CRAN",
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"Hash": "e97c8be593e010f93520e8215c0f9189",
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"Requirements": [
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"bslib",
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"evaluate",
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"htmltools",
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"jquerylib",
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"jsonlite",
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"knitr",
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"stringr",
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"tinytex",
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"xfun",
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"yaml"
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]
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},
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"sass": {
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"Package": "sass",
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"Version": "0.4.2",
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"Source": "Repository",
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"Repository": "CRAN",
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"Hash": "1b191143d7d3444d504277843f3a95fe",
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"Requirements": [
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"R6",
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"fs",
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"htmltools",
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"rappdirs",
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"rlang"
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]
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},
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"shroomDK": {
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"Package": "shroomDK",
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"Version": "0.1.1",
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"Source": "Repository",
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"Repository": "CRAN",
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"Hash": "28b8ac7aa1d889d635c3ac3c5150b11a",
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"Requirements": [
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"httr",
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"jsonlite"
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]
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},
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"stringi": {
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"Package": "stringi",
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"Version": "1.7.8",
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"Source": "Repository",
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"Repository": "CRAN",
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"Hash": "a68b980681bcbc84c7a67003fa796bfb",
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"Requirements": []
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},
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"stringr": {
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"Package": "stringr",
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"Version": "1.4.0",
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"Source": "Repository",
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"Repository": "CRAN",
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||||
"Hash": "0759e6b6c0957edb1311028a49a35e76",
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"Requirements": [
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"glue",
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"magrittr",
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"stringi"
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]
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},
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"sys": {
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"Package": "sys",
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"Version": "3.4",
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"Source": "Repository",
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"Repository": "CRAN",
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"Hash": "b227d13e29222b4574486cfcbde077fa",
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"Requirements": []
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},
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"tinytex": {
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"Package": "tinytex",
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"Version": "0.42",
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"Source": "Repository",
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"Repository": "CRAN",
|
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"Hash": "7629c6c1540835d5248e6e7df265fa74",
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"Requirements": [
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"xfun"
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]
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},
|
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"xfun": {
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"Package": "xfun",
|
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"Version": "0.31",
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"Source": "Repository",
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"Repository": "CRAN",
|
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"Hash": "a318c6f752b8dcfe9fb74d897418ab2b",
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"Requirements": []
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},
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"yaml": {
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"Package": "yaml",
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"Version": "2.3.5",
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"Source": "Repository",
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"Repository": "CRAN",
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"Hash": "458bb38374d73bf83b1bb85e353da200",
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"Requirements": []
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}
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}
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}
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6
renv/.gitignore
vendored
Normal file
6
renv/.gitignore
vendored
Normal file
@ -0,0 +1,6 @@
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library/
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local/
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cellar/
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lock/
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python/
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staging/
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942
renv/activate.R
Normal file
942
renv/activate.R
Normal file
@ -0,0 +1,942 @@
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local({
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# the requested version of renv
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version <- "0.15.5"
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# the project directory
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project <- getwd()
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# figure out whether the autoloader is enabled
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enabled <- local({
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# first, check config option
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override <- getOption("renv.config.autoloader.enabled")
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if (!is.null(override))
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return(override)
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|
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# next, check environment variables
|
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# TODO: prefer using the configuration one in the future
|
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envvars <- c(
|
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"RENV_CONFIG_AUTOLOADER_ENABLED",
|
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"RENV_AUTOLOADER_ENABLED",
|
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"RENV_ACTIVATE_PROJECT"
|
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)
|
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|
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for (envvar in envvars) {
|
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envval <- Sys.getenv(envvar, unset = NA)
|
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if (!is.na(envval))
|
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return(tolower(envval) %in% c("true", "t", "1"))
|
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}
|
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|
||||
# enable by default
|
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TRUE
|
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|
||||
})
|
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|
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if (!enabled)
|
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return(FALSE)
|
||||
|
||||
# avoid recursion
|
||||
if (identical(getOption("renv.autoloader.running"), TRUE)) {
|
||||
warning("ignoring recursive attempt to run renv autoloader")
|
||||
return(invisible(TRUE))
|
||||
}
|
||||
|
||||
# signal that we're loading renv during R startup
|
||||
options(renv.autoloader.running = TRUE)
|
||||
on.exit(options(renv.autoloader.running = NULL), add = TRUE)
|
||||
|
||||
# signal that we've consented to use renv
|
||||
options(renv.consent = TRUE)
|
||||
|
||||
# load the 'utils' package eagerly -- this ensures that renv shims, which
|
||||
# mask 'utils' packages, will come first on the search path
|
||||
library(utils, lib.loc = .Library)
|
||||
|
||||
# unload renv if it's already been loaded
|
||||
if ("renv" %in% loadedNamespaces())
|
||||
unloadNamespace("renv")
|
||||
|
||||
# load bootstrap tools
|
||||
`%||%` <- function(x, y) {
|
||||
if (is.environment(x) || length(x)) x else y
|
||||
}
|
||||
|
||||
bootstrap <- function(version, library) {
|
||||
|
||||
# attempt to download renv
|
||||
tarball <- tryCatch(renv_bootstrap_download(version), error = identity)
|
||||
if (inherits(tarball, "error"))
|
||||
stop("failed to download renv ", version)
|
||||
|
||||
# now attempt to install
|
||||
status <- tryCatch(renv_bootstrap_install(version, tarball, library), error = identity)
|
||||
if (inherits(status, "error"))
|
||||
stop("failed to install renv ", version)
|
||||
|
||||
}
|
||||
|
||||
renv_bootstrap_tests_running <- function() {
|
||||
getOption("renv.tests.running", default = FALSE)
|
||||
}
|
||||
|
||||
renv_bootstrap_repos <- function() {
|
||||
|
||||
# check for repos override
|
||||
repos <- Sys.getenv("RENV_CONFIG_REPOS_OVERRIDE", unset = NA)
|
||||
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@"] <- getOption(
|
||||
"renv.repos.cran",
|
||||
"https://cloud.r-project.org"
|
||||
)
|
||||
|
||||
# add in renv.bootstrap.repos if set
|
||||
default <- c(FALLBACK = "https://cloud.r-project.org")
|
||||
extra <- getOption("renv.bootstrap.repos", default = default)
|
||||
repos <- c(repos, extra)
|
||||
|
||||
# remove duplicates that might've snuck in
|
||||
dupes <- duplicated(repos) | duplicated(names(repos))
|
||||
repos[!dupes]
|
||||
|
||||
}
|
||||
|
||||
renv_bootstrap_repos_lockfile <- function() {
|
||||
|
||||
lockpath <- Sys.getenv("RENV_PATHS_LOCKFILE", unset = "renv.lock")
|
||||
if (!file.exists(lockpath))
|
||||
return(NULL)
|
||||
|
||||
lockfile <- tryCatch(renv_json_read(lockpath), error = identity)
|
||||
if (inherits(lockfile, "error")) {
|
||||
warning(lockfile)
|
||||
return(NULL)
|
||||
}
|
||||
|
||||
repos <- lockfile$R$Repositories
|
||||
if (length(repos) == 0)
|
||||
return(NULL)
|
||||
|
||||
keys <- vapply(repos, `[[`, "Name", FUN.VALUE = character(1))
|
||||
vals <- vapply(repos, `[[`, "URL", FUN.VALUE = character(1))
|
||||
names(vals) <- keys
|
||||
|
||||
return(vals)
|
||||
|
||||
}
|
||||
|
||||
renv_bootstrap_download <- function(version) {
|
||||
|
||||
# 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
|
||||
)
|
||||
)
|
||||
|
||||
for (method in methods) {
|
||||
path <- tryCatch(method(version), error = identity)
|
||||
if (is.character(path) && file.exists(path))
|
||||
return(path)
|
||||
}
|
||||
|
||||
stop("failed to download renv ", version)
|
||||
|
||||
}
|
||||
|
||||
renv_bootstrap_download_impl <- function(url, destfile) {
|
||||
|
||||
mode <- "wb"
|
||||
|
||||
# https://bugs.r-project.org/bugzilla/show_bug.cgi?id=17715
|
||||
fixup <-
|
||||
Sys.info()[["sysname"]] == "Windows" &&
|
||||
substring(url, 1L, 5L) == "file:"
|
||||
|
||||
if (fixup)
|
||||
mode <- "w+b"
|
||||
|
||||
utils::download.file(
|
||||
url = url,
|
||||
destfile = destfile,
|
||||
mode = mode,
|
||||
quiet = TRUE
|
||||
)
|
||||
|
||||
}
|
||||
|
||||
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
|
||||
|
||||
info <- tryCatch(
|
||||
utils::download.packages(
|
||||
pkgs = "renv",
|
||||
destdir = tempdir(),
|
||||
repos = repos,
|
||||
type = type,
|
||||
quiet = TRUE
|
||||
),
|
||||
condition = identity
|
||||
)
|
||||
|
||||
if (inherits(info, "condition")) {
|
||||
message("FAILED")
|
||||
return(FALSE)
|
||||
}
|
||||
|
||||
# report success and return
|
||||
message("OK (downloaded ", type, ")")
|
||||
info[1, 2]
|
||||
|
||||
}
|
||||
|
||||
renv_bootstrap_download_cran_latest_find <- function(version) {
|
||||
|
||||
# check whether binaries are supported on this system
|
||||
binary <-
|
||||
getOption("renv.bootstrap.binary", default = TRUE) &&
|
||||
!identical(.Platform$pkgType, "source") &&
|
||||
!identical(getOption("pkgType"), "source") &&
|
||||
Sys.info()[["sysname"]] %in% c("Darwin", "Windows")
|
||||
|
||||
types <- c(if (binary) "binary", "source")
|
||||
|
||||
# iterate over types + repositories
|
||||
for (type in types) {
|
||||
for (repos in renv_bootstrap_repos()) {
|
||||
|
||||
# retrieve package database
|
||||
db <- tryCatch(
|
||||
as.data.frame(
|
||||
utils::available.packages(type = type, repos = repos),
|
||||
stringsAsFactors = FALSE
|
||||
),
|
||||
error = identity
|
||||
)
|
||||
|
||||
if (inherits(db, "error"))
|
||||
next
|
||||
|
||||
# check for compatible entry
|
||||
entry <- db[db$Package %in% "renv" & db$Version %in% version, ]
|
||||
if (nrow(entry) == 0)
|
||||
next
|
||||
|
||||
# found it; return spec to caller
|
||||
spec <- list(entry = entry, type = type, repos = repos)
|
||||
return(spec)
|
||||
|
||||
}
|
||||
}
|
||||
|
||||
# if we got here, we failed to find renv
|
||||
fmt <- "renv %s is not available from your declared package repositories"
|
||||
stop(sprintf(fmt, version))
|
||||
|
||||
}
|
||||
|
||||
renv_bootstrap_download_cran_archive <- function(version) {
|
||||
|
||||
name <- sprintf("renv_%s.tar.gz", version)
|
||||
repos <- renv_bootstrap_repos()
|
||||
urls <- file.path(repos, "src/contrib/Archive/renv", name)
|
||||
destfile <- file.path(tempdir(), name)
|
||||
|
||||
message("* Downloading renv ", version, " ... ", appendLF = FALSE)
|
||||
|
||||
for (url in urls) {
|
||||
|
||||
status <- tryCatch(
|
||||
renv_bootstrap_download_impl(url, destfile),
|
||||
condition = identity
|
||||
)
|
||||
|
||||
if (identical(status, 0L)) {
|
||||
message("OK")
|
||||
return(destfile)
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
message("FAILED")
|
||||
return(FALSE)
|
||||
|
||||
}
|
||||
|
||||
renv_bootstrap_download_tarball <- function(version) {
|
||||
|
||||
# if the user has provided the path to a tarball via
|
||||
# an environment variable, then use it
|
||||
tarball <- Sys.getenv("RENV_BOOTSTRAP_TARBALL", unset = NA)
|
||||
if (is.na(tarball))
|
||||
return()
|
||||
|
||||
# allow directories
|
||||
info <- file.info(tarball, extra_cols = FALSE)
|
||||
if (identical(info$isdir, TRUE)) {
|
||||
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()
|
||||
|
||||
}
|
||||
|
||||
fmt <- "* Bootstrapping with tarball at path '%s'."
|
||||
msg <- sprintf(fmt, tarball)
|
||||
message(msg)
|
||||
|
||||
tarball
|
||||
|
||||
}
|
||||
|
||||
renv_bootstrap_download_github <- function(version) {
|
||||
|
||||
enabled <- Sys.getenv("RENV_BOOTSTRAP_FROM_GITHUB", unset = "TRUE")
|
||||
if (!identical(enabled, "TRUE"))
|
||||
return(FALSE)
|
||||
|
||||
# prepare download options
|
||||
pat <- Sys.getenv("GITHUB_PAT")
|
||||
if (nzchar(Sys.which("curl")) && nzchar(pat)) {
|
||||
fmt <- "--location --fail --header \"Authorization: token %s\""
|
||||
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(pat)) {
|
||||
fmt <- "--header=\"Authorization: token %s\""
|
||||
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)
|
||||
|
||||
status <- tryCatch(
|
||||
renv_bootstrap_download_impl(url, destfile),
|
||||
condition = identity
|
||||
)
|
||||
|
||||
if (!identical(status, 0L)) {
|
||||
message("FAILED")
|
||||
return(FALSE)
|
||||
}
|
||||
|
||||
message("OK")
|
||||
return(destfile)
|
||||
|
||||
}
|
||||
|
||||
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)
|
||||
|
||||
# invoke using system2 so we can capture and report output
|
||||
bin <- R.home("bin")
|
||||
exe <- if (Sys.info()[["sysname"]] == "Windows") "R.exe" else "R"
|
||||
r <- file.path(bin, exe)
|
||||
|
||||
args <- c(
|
||||
"--vanilla", "CMD", "INSTALL", "--no-multiarch",
|
||||
"-l", shQuote(path.expand(library)),
|
||||
shQuote(path.expand(tarball))
|
||||
)
|
||||
|
||||
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
|
||||
|
||||
}
|
||||
|
||||
renv_bootstrap_platform_prefix <- function() {
|
||||
|
||||
# construct version prefix
|
||||
version <- paste(R.version$major, R.version$minor, sep = ".")
|
||||
prefix <- paste("R", numeric_version(version)[1, 1:2], sep = "-")
|
||||
|
||||
# include SVN revision for development versions of R
|
||||
# (to avoid sharing platform-specific artefacts with released versions of R)
|
||||
devel <-
|
||||
identical(R.version[["status"]], "Under development (unstable)") ||
|
||||
identical(R.version[["nickname"]], "Unsuffered Consequences")
|
||||
|
||||
if (devel)
|
||||
prefix <- paste(prefix, R.version[["svn rev"]], sep = "-r")
|
||||
|
||||
# build list of path components
|
||||
components <- c(prefix, R.version$platform)
|
||||
|
||||
# include prefix if provided by user
|
||||
prefix <- renv_bootstrap_platform_prefix_impl()
|
||||
if (!is.na(prefix) && nzchar(prefix))
|
||||
components <- c(prefix, components)
|
||||
|
||||
# build prefix
|
||||
paste(components, collapse = "/")
|
||||
|
||||
}
|
||||
|
||||
renv_bootstrap_platform_prefix_impl <- function() {
|
||||
|
||||
# if an explicit prefix has been supplied, use it
|
||||
prefix <- Sys.getenv("RENV_PATHS_PREFIX", unset = NA)
|
||||
if (!is.na(prefix))
|
||||
return(prefix)
|
||||
|
||||
# if the user has requested an automatic prefix, generate it
|
||||
auto <- Sys.getenv("RENV_PATHS_PREFIX_AUTO", unset = NA)
|
||||
if (auto %in% c("TRUE", "True", "true", "1"))
|
||||
return(renv_bootstrap_platform_prefix_auto())
|
||||
|
||||
# empty string on failure
|
||||
""
|
||||
|
||||
}
|
||||
|
||||
renv_bootstrap_platform_prefix_auto <- function() {
|
||||
|
||||
prefix <- tryCatch(renv_bootstrap_platform_os(), error = identity)
|
||||
if (inherits(prefix, "error") || prefix %in% "unknown") {
|
||||
|
||||
msg <- paste(
|
||||
"failed to infer current operating system",
|
||||
"please file a bug report at https://github.com/rstudio/renv/issues",
|
||||
sep = "; "
|
||||
)
|
||||
|
||||
warning(msg)
|
||||
|
||||
}
|
||||
|
||||
prefix
|
||||
|
||||
}
|
||||
|
||||
renv_bootstrap_platform_os <- function() {
|
||||
|
||||
sysinfo <- Sys.info()
|
||||
sysname <- sysinfo[["sysname"]]
|
||||
|
||||
# handle Windows + macOS up front
|
||||
if (sysname == "Windows")
|
||||
return("windows")
|
||||
else if (sysname == "Darwin")
|
||||
return("macos")
|
||||
|
||||
# check for os-release files
|
||||
for (file in c("/etc/os-release", "/usr/lib/os-release"))
|
||||
if (file.exists(file))
|
||||
return(renv_bootstrap_platform_os_via_os_release(file, sysinfo))
|
||||
|
||||
# check for redhat-release files
|
||||
if (file.exists("/etc/redhat-release"))
|
||||
return(renv_bootstrap_platform_os_via_redhat_release())
|
||||
|
||||
"unknown"
|
||||
|
||||
}
|
||||
|
||||
renv_bootstrap_platform_os_via_os_release <- function(file, sysinfo) {
|
||||
|
||||
# read /etc/os-release
|
||||
release <- utils::read.table(
|
||||
file = file,
|
||||
sep = "=",
|
||||
quote = c("\"", "'"),
|
||||
col.names = c("Key", "Value"),
|
||||
comment.char = "#",
|
||||
stringsAsFactors = FALSE
|
||||
)
|
||||
|
||||
vars <- as.list(release$Value)
|
||||
names(vars) <- release$Key
|
||||
|
||||
# get os name
|
||||
os <- tolower(sysinfo[["sysname"]])
|
||||
|
||||
# read id
|
||||
id <- "unknown"
|
||||
for (field in c("ID", "ID_LIKE")) {
|
||||
if (field %in% names(vars) && nzchar(vars[[field]])) {
|
||||
id <- vars[[field]]
|
||||
break
|
||||
}
|
||||
}
|
||||
|
||||
# read version
|
||||
version <- "unknown"
|
||||
for (field in c("UBUNTU_CODENAME", "VERSION_CODENAME", "VERSION_ID", "BUILD_ID")) {
|
||||
if (field %in% names(vars) && nzchar(vars[[field]])) {
|
||||
version <- vars[[field]]
|
||||
break
|
||||
}
|
||||
}
|
||||
|
||||
# join together
|
||||
paste(c(os, id, version), collapse = "-")
|
||||
|
||||
}
|
||||
|
||||
renv_bootstrap_platform_os_via_redhat_release <- function() {
|
||||
|
||||
# read /etc/redhat-release
|
||||
contents <- readLines("/etc/redhat-release", warn = FALSE)
|
||||
|
||||
# infer id
|
||||
id <- if (grepl("centos", contents, ignore.case = TRUE))
|
||||
"centos"
|
||||
else if (grepl("redhat", contents, ignore.case = TRUE))
|
||||
"redhat"
|
||||
else
|
||||
"unknown"
|
||||
|
||||
# try to find a version component (very hacky)
|
||||
version <- "unknown"
|
||||
|
||||
parts <- strsplit(contents, "[[:space:]]")[[1L]]
|
||||
for (part in parts) {
|
||||
|
||||
nv <- tryCatch(numeric_version(part), error = identity)
|
||||
if (inherits(nv, "error"))
|
||||
next
|
||||
|
||||
version <- nv[1, 1]
|
||||
break
|
||||
|
||||
}
|
||||
|
||||
paste(c("linux", id, version), collapse = "-")
|
||||
|
||||
}
|
||||
|
||||
renv_bootstrap_library_root_name <- function(project) {
|
||||
|
||||
# use project name as-is if requested
|
||||
asis <- Sys.getenv("RENV_PATHS_LIBRARY_ROOT_ASIS", unset = "FALSE")
|
||||
if (asis)
|
||||
return(basename(project))
|
||||
|
||||
# otherwise, disambiguate based on project's path
|
||||
id <- substring(renv_bootstrap_hash_text(project), 1L, 8L)
|
||||
paste(basename(project), id, sep = "-")
|
||||
|
||||
}
|
||||
|
||||
renv_bootstrap_library_root <- function(project) {
|
||||
|
||||
prefix <- renv_bootstrap_profile_prefix()
|
||||
|
||||
path <- Sys.getenv("RENV_PATHS_LIBRARY", unset = NA)
|
||||
if (!is.na(path))
|
||||
return(paste(c(path, prefix), collapse = "/"))
|
||||
|
||||
path <- renv_bootstrap_library_root_impl(project)
|
||||
if (!is.null(path)) {
|
||||
name <- renv_bootstrap_library_root_name(project)
|
||||
return(paste(c(path, prefix, name), collapse = "/"))
|
||||
}
|
||||
|
||||
renv_bootstrap_paths_renv("library", project = project)
|
||||
|
||||
}
|
||||
|
||||
renv_bootstrap_library_root_impl <- function(project) {
|
||||
|
||||
root <- Sys.getenv("RENV_PATHS_LIBRARY_ROOT", unset = NA)
|
||||
if (!is.na(root))
|
||||
return(root)
|
||||
|
||||
type <- renv_bootstrap_project_type(project)
|
||||
if (identical(type, "package")) {
|
||||
userdir <- renv_bootstrap_user_dir()
|
||||
return(file.path(userdir, "library"))
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
renv_bootstrap_validate_version <- function(version) {
|
||||
|
||||
loadedversion <- utils::packageDescription("renv", fields = "Version")
|
||||
if (version == loadedversion)
|
||||
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 = "@")
|
||||
else
|
||||
paste("renv", loadedversion, 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"
|
||||
)
|
||||
|
||||
msg <- sprintf(fmt, loadedversion, version, remote)
|
||||
warning(msg, call. = FALSE)
|
||||
|
||||
FALSE
|
||||
|
||||
}
|
||||
|
||||
renv_bootstrap_hash_text <- function(text) {
|
||||
|
||||
hashfile <- tempfile("renv-hash-")
|
||||
on.exit(unlink(hashfile), add = TRUE)
|
||||
|
||||
writeLines(text, con = hashfile)
|
||||
tools::md5sum(hashfile)
|
||||
|
||||
}
|
||||
|
||||
renv_bootstrap_load <- function(project, libpath, version) {
|
||||
|
||||
# try to load renv from the project library
|
||||
if (!requireNamespace("renv", lib.loc = libpath, quietly = TRUE))
|
||||
return(FALSE)
|
||||
|
||||
# warn if the version of renv loaded does not match
|
||||
renv_bootstrap_validate_version(version)
|
||||
|
||||
# load the project
|
||||
renv::load(project)
|
||||
|
||||
TRUE
|
||||
|
||||
}
|
||||
|
||||
renv_bootstrap_profile_load <- function(project) {
|
||||
|
||||
# if RENV_PROFILE is already set, just use that
|
||||
profile <- Sys.getenv("RENV_PROFILE", unset = NA)
|
||||
if (!is.na(profile) && nzchar(profile))
|
||||
return(profile)
|
||||
|
||||
# check for a profile file (nothing to do if it doesn't exist)
|
||||
path <- renv_bootstrap_paths_renv("profile", profile = FALSE)
|
||||
if (!file.exists(path))
|
||||
return(NULL)
|
||||
|
||||
# read the profile, and set it if it exists
|
||||
contents <- readLines(path, warn = FALSE)
|
||||
if (length(contents) == 0L)
|
||||
return(NULL)
|
||||
|
||||
# set RENV_PROFILE
|
||||
profile <- contents[[1L]]
|
||||
if (!profile %in% c("", "default"))
|
||||
Sys.setenv(RENV_PROFILE = profile)
|
||||
|
||||
profile
|
||||
|
||||
}
|
||||
|
||||
renv_bootstrap_profile_prefix <- function() {
|
||||
profile <- renv_bootstrap_profile_get()
|
||||
if (!is.null(profile))
|
||||
return(file.path("profiles", profile, "renv"))
|
||||
}
|
||||
|
||||
renv_bootstrap_profile_get <- function() {
|
||||
profile <- Sys.getenv("RENV_PROFILE", unset = "")
|
||||
renv_bootstrap_profile_normalize(profile)
|
||||
}
|
||||
|
||||
renv_bootstrap_profile_set <- function(profile) {
|
||||
profile <- renv_bootstrap_profile_normalize(profile)
|
||||
if (is.null(profile))
|
||||
Sys.unsetenv("RENV_PROFILE")
|
||||
else
|
||||
Sys.setenv(RENV_PROFILE = profile)
|
||||
}
|
||||
|
||||
renv_bootstrap_profile_normalize <- function(profile) {
|
||||
|
||||
if (is.null(profile) || profile %in% c("", "default"))
|
||||
return(NULL)
|
||||
|
||||
profile
|
||||
|
||||
}
|
||||
|
||||
renv_bootstrap_path_absolute <- function(path) {
|
||||
|
||||
substr(path, 1L, 1L) %in% c("~", "/", "\\") || (
|
||||
substr(path, 1L, 1L) %in% c(letters, LETTERS) &&
|
||||
substr(path, 2L, 3L) %in% c(":/", ":\\")
|
||||
)
|
||||
|
||||
}
|
||||
|
||||
renv_bootstrap_paths_renv <- function(..., profile = TRUE, project = NULL) {
|
||||
renv <- Sys.getenv("RENV_PATHS_RENV", unset = "renv")
|
||||
root <- if (renv_bootstrap_path_absolute(renv)) NULL else project
|
||||
prefix <- if (profile) renv_bootstrap_profile_prefix()
|
||||
components <- c(root, renv, prefix, ...)
|
||||
paste(components, collapse = "/")
|
||||
}
|
||||
|
||||
renv_bootstrap_project_type <- function(path) {
|
||||
|
||||
descpath <- file.path(path, "DESCRIPTION")
|
||||
if (!file.exists(descpath))
|
||||
return("unknown")
|
||||
|
||||
desc <- tryCatch(
|
||||
read.dcf(descpath, all = TRUE),
|
||||
error = identity
|
||||
)
|
||||
|
||||
if (inherits(desc, "error"))
|
||||
return("unknown")
|
||||
|
||||
type <- desc$Type
|
||||
if (!is.null(type))
|
||||
return(tolower(type))
|
||||
|
||||
package <- desc$Package
|
||||
if (!is.null(package))
|
||||
return("package")
|
||||
|
||||
"unknown"
|
||||
|
||||
}
|
||||
|
||||
renv_bootstrap_user_dir <- function() {
|
||||
dir <- renv_bootstrap_user_dir_impl()
|
||||
path.expand(chartr("\\", "/", dir))
|
||||
}
|
||||
|
||||
renv_bootstrap_user_dir_impl <- function() {
|
||||
|
||||
# use local override if set
|
||||
override <- getOption("renv.userdir.override")
|
||||
if (!is.null(override))
|
||||
return(override)
|
||||
|
||||
# use R_user_dir if available
|
||||
tools <- asNamespace("tools")
|
||||
if (is.function(tools$R_user_dir))
|
||||
return(tools$R_user_dir("renv", "cache"))
|
||||
|
||||
# try using our own backfill for older versions of R
|
||||
envvars <- c("R_USER_CACHE_DIR", "XDG_CACHE_HOME")
|
||||
for (envvar in envvars) {
|
||||
root <- Sys.getenv(envvar, unset = NA)
|
||||
if (!is.na(root))
|
||||
return(file.path(root, "R/renv"))
|
||||
}
|
||||
|
||||
# use platform-specific default fallbacks
|
||||
if (Sys.info()[["sysname"]] == "Windows")
|
||||
file.path(Sys.getenv("LOCALAPPDATA"), "R/cache/R/renv")
|
||||
else if (Sys.info()[["sysname"]] == "Darwin")
|
||||
"~/Library/Caches/org.R-project.R/R/renv"
|
||||
else
|
||||
"~/.cache/R/renv"
|
||||
|
||||
}
|
||||
|
||||
|
||||
renv_json_read <- function(file = NULL, text = NULL) {
|
||||
|
||||
text <- paste(text %||% read(file), collapse = "\n")
|
||||
|
||||
# find strings in the JSON
|
||||
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("[[{]", "list(", transformed)
|
||||
transformed <- gsub("[]}]", ")", transformed)
|
||||
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_remap(json, map)
|
||||
|
||||
# evaluate
|
||||
eval(remapped, envir = baseenv())
|
||||
|
||||
}
|
||||
|
||||
renv_json_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_remap(json[[i]], map))
|
||||
}
|
||||
}
|
||||
|
||||
json
|
||||
|
||||
}
|
||||
|
||||
# load the renv profile, if any
|
||||
renv_bootstrap_profile_load(project)
|
||||
|
||||
# construct path to library root
|
||||
root <- renv_bootstrap_library_root(project)
|
||||
|
||||
# construct library prefix for platform
|
||||
prefix <- renv_bootstrap_platform_prefix()
|
||||
|
||||
# construct full libpath
|
||||
libpath <- file.path(root, prefix)
|
||||
|
||||
# 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."
|
||||
)
|
||||
|
||||
warning(paste(msg, collapse = "\n"), call. = FALSE)
|
||||
|
||||
})
|
||||
10
renv/settings.dcf
Normal file
10
renv/settings.dcf
Normal file
@ -0,0 +1,10 @@
|
||||
bioconductor.version:
|
||||
external.libraries:
|
||||
ignored.packages:
|
||||
package.dependency.fields: Imports, Depends, LinkingTo
|
||||
r.version:
|
||||
snapshot.type: implicit
|
||||
use.cache: TRUE
|
||||
vcs.ignore.cellar: TRUE
|
||||
vcs.ignore.library: TRUE
|
||||
vcs.ignore.local: TRUE
|
||||
19
template.Rmd
19
template.Rmd
@ -14,4 +14,21 @@ editor_options:
|
||||
chunk_output_type: console
|
||||
---
|
||||
|
||||
# Intro
|
||||
# Intro
|
||||
|
||||
This is the Flipside Crypto RMarkdown template. It includes an renv lockfile with shroomDK.
|
||||
Please ensure renv is installed on your machine and use the provided chunk (click Show Code) to begin.
|
||||
|
||||
To use this template:
|
||||
|
||||
1. Clone this repo into a new repo
|
||||
2. Rename the R Project
|
||||
3. Rename the template Rmd file
|
||||
4. Restore the r environment
|
||||
5. Push your new repo with new file names.
|
||||
6. Begin working! You can edit the header, footer, and styles.css file as needed, some defaults are provided. Use Knit to HTML to view the effects of these defaults.
|
||||
|
||||
```{r}
|
||||
renv::restore()
|
||||
library(shroomDK)
|
||||
```
|
||||
Loading…
Reference in New Issue
Block a user