mirror of
https://github.com/FlipsideCrypto/onchain-pricing.git
synced 2026-02-06 10:56:48 +00:00
initiate
This commit is contained in:
Carlos R. Mercado
commit
08ba3a37d4
5
.gitignore
vendored
Normal file
5
.gitignore
vendored
Normal file
@ -0,0 +1,5 @@
|
||||
.Rproj.user
|
||||
.Rhistory
|
||||
.RData
|
||||
.Ruserdata
|
||||
api_key.txt
|
||||
BIN
FLIPSIDE-BRAND-1-BLACK.png
Normal file
BIN
FLIPSIDE-BRAND-1-BLACK.png
Normal file
Binary file not shown.
|
After Width: | Height: | Size: 8.6 KiB |
BIN
FLIPSIDE-BRAND-1-WHITE.png
Normal file
BIN
FLIPSIDE-BRAND-1-WHITE.png
Normal file
Binary file not shown.
|
After Width: | Height: | Size: 8.0 KiB |
21
LICENSE
Normal file
21
LICENSE
Normal file
@ -0,0 +1,21 @@
|
||||
MIT License
|
||||
|
||||
Copyright (c) 2022 Carlos R. Mercado
|
||||
|
||||
Permission is hereby granted, free of charge, to any person obtaining a copy
|
||||
of this software and associated documentation files (the "Software"), to deal
|
||||
in the Software without restriction, including without limitation the rights
|
||||
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
|
||||
copies of the Software, and to permit persons to whom the Software is
|
||||
furnished to do so, subject to the following conditions:
|
||||
|
||||
The above copyright notice and this permission notice shall be included in all
|
||||
copies or substantial portions of the Software.
|
||||
|
||||
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
|
||||
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
|
||||
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
|
||||
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
|
||||
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
|
||||
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
|
||||
SOFTWARE.
|
||||
51
README.md
Normal file
51
README.md
Normal file
@ -0,0 +1,51 @@
|
||||
# Topic: Onchain-Pricing
|
||||
|
||||
For any reproducible analysis using this template please follow the provided format.
|
||||
|
||||
1. 2-3 sentence summary of the analysis.
|
||||
2. Link to both the general research site & specific report on that research site. A markdown example is provided to show how to link using `[]()` syntax. Details on how to update the research site are available [at its repo](https://github.com/FlipsideCrypto/research).
|
||||
|
||||
`For a deeper dive into the context, you can check out the report on our [research site](https://science.flipsidecrypto.xyz/research/) at [bonk-post-mortem](https://science.flipsidecrypto.xyz/bonk-post-mortem/).`
|
||||
|
||||
3. Link to the email sized version of the analysis on the flipside beehiiv. A markdown example is provided showing how to use the `[]()` syntax and identify the beehiiv site. To add content to the beehiiv site, please contact the beehiiv admin to get added as an org member.
|
||||
|
||||
`If you aren't interested in code and want the shortest summary of the situation, you can check out the email sized [bonk-post-mortem](https://flipsidecrypto.beehiiv.com/p/bonk-post-mortem) on our research beehiiv and subscribe to get (summaries of) the best crypto research direct to your inbox.`
|
||||
|
||||
4. Keep the Reproduce Analysis section (confirm links work) with the shroomDK and renv subheaders. Confirm your analysis is reproducible by using renv and that any SQL code you used to pull data is provided and accessible via shroomDK. For Python analysis use `pyenv` and `pip install shroomdk` and swap out any R details for Python ones.
|
||||
|
||||
5. Update the instructions section.
|
||||
|
||||
- To keep code bases uniform, please use `readLines('api_key.txt')` to access your api key within code and ensure gitignore files are consistently able to keep API Keys off github.
|
||||
|
||||
- Use R Projects & renv to ensure portability across directories and operating systems.
|
||||
|
||||
- For analysis across multiple files; either provide a single .Rmd file that accesses those files in order or explicitly detail what order .R files should be run in.
|
||||
|
||||
# Reproduce Analysis
|
||||
|
||||
All analysis is reproducible using the R programming language. You'll need (1) an shroomDK API key to copy our SQL queries and extract data from the [FlipsideCrypto data app](https://next.flipsidecrypto.xyz/); and (2) renv to get the exact package versions we used.
|
||||
|
||||
## shroomDK
|
||||
|
||||
shroomDK is an R package that accesses the FlipsideCrypto REST API; it is also available for Python. You pass SQL code as a string to our API and get up to 1M rows of data back!
|
||||
|
||||
Check out the [documentation](https://docs.flipsidecrypto.com/shroomdk-sdk/get-started) and get your free API Key today.
|
||||
|
||||
## renv
|
||||
|
||||
renv is a package manager for the R programming language. It ensures analysis is fully reproducible by tracking the exact package versions used in the analysis.
|
||||
|
||||
`install.packages('renv')`
|
||||
|
||||
## Instructions
|
||||
|
||||
To replicate this analysis please do the following:
|
||||
|
||||
1. Clone this repo.
|
||||
2. Save your API key into a .txt file as 'api_key.txt' (this exact naming allows the provided .gitignore to ignore your key and keep it off github).
|
||||
3. Open the `R PROJECT NAME HERE` R Project file in your R IDE (we recommend, RStudio).
|
||||
4. Confirm you have renv installed.
|
||||
5. Restore the R environment using `renv::restore()` while in the `R PROJECT NAME HERE` R Project.
|
||||
6. You can now run `SPECIFY .R FILE(s) and/or .Rmd FILE(s) HERE`
|
||||
|
||||
If any errors arise, double check you have saved your API key in the expected file name and format.
|
||||
0
footer.html
Normal file
0
footer.html
Normal file
3
header.html
Normal file
3
header.html
Normal file
@ -0,0 +1,3 @@
|
||||
<head>
|
||||
<a href="https://science.flipsidecrypto.xyz/research"><img src="FLIPSIDE-BRAND-1-WHITE.png"></a>
|
||||
</head>
|
||||
19
onchain-pricing.Rmd
Normal file
19
onchain-pricing.Rmd
Normal file
@ -0,0 +1,19 @@
|
||||
---
|
||||
title: "On-Chain Pricing"
|
||||
author: "Charliemarketplace"
|
||||
date: "`r Sys.Date()`"
|
||||
output:
|
||||
html_document:
|
||||
css: "styles.css"
|
||||
includes:
|
||||
in_header: header.html
|
||||
code_folding: hide
|
||||
toc: true
|
||||
toc_float: true
|
||||
editor_options:
|
||||
chunk_output_type: console
|
||||
---
|
||||
|
||||
FlipsideCrypto's Research is open source. Check out all the code for this report [here](https://github.com/FlipsideCrypto/onchain-pricing) on github.
|
||||
|
||||
# Intro
|
||||
13
onchain-pricing.Rproj
Normal file
13
onchain-pricing.Rproj
Normal file
@ -0,0 +1,13 @@
|
||||
Version: 1.0
|
||||
|
||||
RestoreWorkspace: Default
|
||||
SaveWorkspace: Default
|
||||
AlwaysSaveHistory: Default
|
||||
|
||||
EnableCodeIndexing: Yes
|
||||
UseSpacesForTab: Yes
|
||||
NumSpacesForTab: 2
|
||||
Encoding: UTF-8
|
||||
|
||||
RnwWeave: Sweave
|
||||
LaTeX: pdfLaTeX
|
||||
392
renv.lock
Normal file
392
renv.lock
Normal file
@ -0,0 +1,392 @@
|
||||
{
|
||||
"R": {
|
||||
"Version": "4.2.1",
|
||||
"Repositories": [
|
||||
{
|
||||
"Name": "CRAN",
|
||||
"URL": "https://cran.rstudio.com"
|
||||
}
|
||||
]
|
||||
},
|
||||
"Packages": {
|
||||
"R6": {
|
||||
"Package": "R6",
|
||||
"Version": "2.5.1",
|
||||
"Source": "Repository",
|
||||
"Repository": "CRAN",
|
||||
"Hash": "470851b6d5d0ac559e9d01bb352b4021",
|
||||
"Requirements": []
|
||||
},
|
||||
"askpass": {
|
||||
"Package": "askpass",
|
||||
"Version": "1.1",
|
||||
"Source": "Repository",
|
||||
"Repository": "CRAN",
|
||||
"Hash": "e8a22846fff485f0be3770c2da758713",
|
||||
"Requirements": [
|
||||
"sys"
|
||||
]
|
||||
},
|
||||
"base64enc": {
|
||||
"Package": "base64enc",
|
||||
"Version": "0.1-3",
|
||||
"Source": "Repository",
|
||||
"Repository": "CRAN",
|
||||
"Hash": "543776ae6848fde2f48ff3816d0628bc",
|
||||
"Requirements": []
|
||||
},
|
||||
"bslib": {
|
||||
"Package": "bslib",
|
||||
"Version": "0.4.2",
|
||||
"Source": "Repository",
|
||||
"Repository": "CRAN",
|
||||
"Hash": "a7fbf03946ad741129dc81098722fca1",
|
||||
"Requirements": [
|
||||
"base64enc",
|
||||
"cachem",
|
||||
"htmltools",
|
||||
"jquerylib",
|
||||
"jsonlite",
|
||||
"memoise",
|
||||
"mime",
|
||||
"rlang",
|
||||
"sass"
|
||||
]
|
||||
},
|
||||
"cachem": {
|
||||
"Package": "cachem",
|
||||
"Version": "1.0.6",
|
||||
"Source": "Repository",
|
||||
"Repository": "CRAN",
|
||||
"Hash": "648c5b3d71e6a37e3043617489a0a0e9",
|
||||
"Requirements": [
|
||||
"fastmap",
|
||||
"rlang"
|
||||
]
|
||||
},
|
||||
"cli": {
|
||||
"Package": "cli",
|
||||
"Version": "3.6.0",
|
||||
"Source": "Repository",
|
||||
"Repository": "CRAN",
|
||||
"Hash": "3177a5a16c243adc199ba33117bd9657",
|
||||
"Requirements": []
|
||||
},
|
||||
"curl": {
|
||||
"Package": "curl",
|
||||
"Version": "5.0.0",
|
||||
"Source": "Repository",
|
||||
"Repository": "CRAN",
|
||||
"Hash": "e4f97056611e8e6b8b852d13b7400cf1",
|
||||
"Requirements": []
|
||||
},
|
||||
"digest": {
|
||||
"Package": "digest",
|
||||
"Version": "0.6.31",
|
||||
"Source": "Repository",
|
||||
"Repository": "CRAN",
|
||||
"Hash": "8b708f296afd9ae69f450f9640be8990",
|
||||
"Requirements": []
|
||||
},
|
||||
"ellipsis": {
|
||||
"Package": "ellipsis",
|
||||
"Version": "0.3.2",
|
||||
"Source": "Repository",
|
||||
"Repository": "CRAN",
|
||||
"Hash": "bb0eec2fe32e88d9e2836c2f73ea2077",
|
||||
"Requirements": [
|
||||
"rlang"
|
||||
]
|
||||
},
|
||||
"evaluate": {
|
||||
"Package": "evaluate",
|
||||
"Version": "0.20",
|
||||
"Source": "Repository",
|
||||
"Repository": "CRAN",
|
||||
"Hash": "4b68aa51edd89a0e044a66e75ae3cc6c",
|
||||
"Requirements": []
|
||||
},
|
||||
"fastmap": {
|
||||
"Package": "fastmap",
|
||||
"Version": "1.1.0",
|
||||
"Source": "Repository",
|
||||
"Repository": "CRAN",
|
||||
"Hash": "77bd60a6157420d4ffa93b27cf6a58b8",
|
||||
"Requirements": []
|
||||
},
|
||||
"fs": {
|
||||
"Package": "fs",
|
||||
"Version": "1.5.2",
|
||||
"Source": "Repository",
|
||||
"Repository": "CRAN",
|
||||
"Hash": "7c89603d81793f0d5486d91ab1fc6f1d",
|
||||
"Requirements": []
|
||||
},
|
||||
"glue": {
|
||||
"Package": "glue",
|
||||
"Version": "1.6.2",
|
||||
"Source": "Repository",
|
||||
"Repository": "CRAN",
|
||||
"Hash": "4f2596dfb05dac67b9dc558e5c6fba2e",
|
||||
"Requirements": []
|
||||
},
|
||||
"highr": {
|
||||
"Package": "highr",
|
||||
"Version": "0.10",
|
||||
"Source": "Repository",
|
||||
"Repository": "CRAN",
|
||||
"Hash": "06230136b2d2b9ba5805e1963fa6e890",
|
||||
"Requirements": [
|
||||
"xfun"
|
||||
]
|
||||
},
|
||||
"htmltools": {
|
||||
"Package": "htmltools",
|
||||
"Version": "0.5.4",
|
||||
"Source": "Repository",
|
||||
"Repository": "CRAN",
|
||||
"Hash": "9d27e99cc90bd701c0a7a63e5923f9b7",
|
||||
"Requirements": [
|
||||
"base64enc",
|
||||
"digest",
|
||||
"ellipsis",
|
||||
"fastmap",
|
||||
"rlang"
|
||||
]
|
||||
},
|
||||
"httr": {
|
||||
"Package": "httr",
|
||||
"Version": "1.4.4",
|
||||
"Source": "Repository",
|
||||
"Repository": "CRAN",
|
||||
"Hash": "57557fac46471f0dbbf44705cc6a5c8c",
|
||||
"Requirements": [
|
||||
"R6",
|
||||
"curl",
|
||||
"jsonlite",
|
||||
"mime",
|
||||
"openssl"
|
||||
]
|
||||
},
|
||||
"jquerylib": {
|
||||
"Package": "jquerylib",
|
||||
"Version": "0.1.4",
|
||||
"Source": "Repository",
|
||||
"Repository": "CRAN",
|
||||
"Hash": "5aab57a3bd297eee1c1d862735972182",
|
||||
"Requirements": [
|
||||
"htmltools"
|
||||
]
|
||||
},
|
||||
"jsonlite": {
|
||||
"Package": "jsonlite",
|
||||
"Version": "1.8.4",
|
||||
"Source": "Repository",
|
||||
"Repository": "CRAN",
|
||||
"Hash": "a4269a09a9b865579b2635c77e572374",
|
||||
"Requirements": []
|
||||
},
|
||||
"knitr": {
|
||||
"Package": "knitr",
|
||||
"Version": "1.41",
|
||||
"Source": "Repository",
|
||||
"Repository": "CRAN",
|
||||
"Hash": "6d4971f3610e75220534a1befe81bc92",
|
||||
"Requirements": [
|
||||
"evaluate",
|
||||
"highr",
|
||||
"stringr",
|
||||
"xfun",
|
||||
"yaml"
|
||||
]
|
||||
},
|
||||
"lifecycle": {
|
||||
"Package": "lifecycle",
|
||||
"Version": "1.0.3",
|
||||
"Source": "Repository",
|
||||
"Repository": "CRAN",
|
||||
"Hash": "001cecbeac1cff9301bdc3775ee46a86",
|
||||
"Requirements": [
|
||||
"cli",
|
||||
"glue",
|
||||
"rlang"
|
||||
]
|
||||
},
|
||||
"magrittr": {
|
||||
"Package": "magrittr",
|
||||
"Version": "2.0.3",
|
||||
"Source": "Repository",
|
||||
"Repository": "CRAN",
|
||||
"Hash": "7ce2733a9826b3aeb1775d56fd305472",
|
||||
"Requirements": []
|
||||
},
|
||||
"memoise": {
|
||||
"Package": "memoise",
|
||||
"Version": "2.0.1",
|
||||
"Source": "Repository",
|
||||
"Repository": "CRAN",
|
||||
"Hash": "e2817ccf4a065c5d9d7f2cfbe7c1d78c",
|
||||
"Requirements": [
|
||||
"cachem",
|
||||
"rlang"
|
||||
]
|
||||
},
|
||||
"mime": {
|
||||
"Package": "mime",
|
||||
"Version": "0.12",
|
||||
"Source": "Repository",
|
||||
"Repository": "CRAN",
|
||||
"Hash": "18e9c28c1d3ca1560ce30658b22ce104",
|
||||
"Requirements": []
|
||||
},
|
||||
"openssl": {
|
||||
"Package": "openssl",
|
||||
"Version": "2.0.5",
|
||||
"Source": "Repository",
|
||||
"Repository": "CRAN",
|
||||
"Hash": "b04c27110bf367b4daa93f34f3d58e75",
|
||||
"Requirements": [
|
||||
"askpass"
|
||||
]
|
||||
},
|
||||
"rappdirs": {
|
||||
"Package": "rappdirs",
|
||||
"Version": "0.3.3",
|
||||
"Source": "Repository",
|
||||
"Repository": "CRAN",
|
||||
"Hash": "5e3c5dc0b071b21fa128676560dbe94d",
|
||||
"Requirements": []
|
||||
},
|
||||
"renv": {
|
||||
"Package": "renv",
|
||||
"Version": "0.15.5",
|
||||
"Source": "Repository",
|
||||
"Repository": "CRAN",
|
||||
"Hash": "6a38294e7d12f5d8e656b08c5bd8ae34",
|
||||
"Requirements": []
|
||||
},
|
||||
"rlang": {
|
||||
"Package": "rlang",
|
||||
"Version": "1.0.6",
|
||||
"Source": "Repository",
|
||||
"Repository": "CRAN",
|
||||
"Hash": "4ed1f8336c8d52c3e750adcdc57228a7",
|
||||
"Requirements": []
|
||||
},
|
||||
"rmarkdown": {
|
||||
"Package": "rmarkdown",
|
||||
"Version": "2.19",
|
||||
"Source": "Repository",
|
||||
"Repository": "CRAN",
|
||||
"Hash": "4e29299e1f4c7eabb0b8365b338adf3c",
|
||||
"Requirements": [
|
||||
"bslib",
|
||||
"evaluate",
|
||||
"htmltools",
|
||||
"jquerylib",
|
||||
"jsonlite",
|
||||
"knitr",
|
||||
"stringr",
|
||||
"tinytex",
|
||||
"xfun",
|
||||
"yaml"
|
||||
]
|
||||
},
|
||||
"sass": {
|
||||
"Package": "sass",
|
||||
"Version": "0.4.4",
|
||||
"Source": "Repository",
|
||||
"Repository": "CRAN",
|
||||
"Hash": "c76cbac7ca04ce82d8c38e29729987a3",
|
||||
"Requirements": [
|
||||
"R6",
|
||||
"fs",
|
||||
"htmltools",
|
||||
"rappdirs",
|
||||
"rlang"
|
||||
]
|
||||
},
|
||||
"shroomDK": {
|
||||
"Package": "shroomDK",
|
||||
"Version": "0.1.1",
|
||||
"Source": "Repository",
|
||||
"Repository": "CRAN",
|
||||
"Hash": "28b8ac7aa1d889d635c3ac3c5150b11a",
|
||||
"Requirements": [
|
||||
"httr",
|
||||
"jsonlite"
|
||||
]
|
||||
},
|
||||
"stringi": {
|
||||
"Package": "stringi",
|
||||
"Version": "1.7.12",
|
||||
"Source": "Repository",
|
||||
"Repository": "CRAN",
|
||||
"Hash": "ca8bd84263c77310739d2cf64d84d7c9",
|
||||
"Requirements": []
|
||||
},
|
||||
"stringr": {
|
||||
"Package": "stringr",
|
||||
"Version": "1.5.0",
|
||||
"Source": "Repository",
|
||||
"Repository": "CRAN",
|
||||
"Hash": "671a4d384ae9d32fc47a14e98bfa3dc8",
|
||||
"Requirements": [
|
||||
"cli",
|
||||
"glue",
|
||||
"lifecycle",
|
||||
"magrittr",
|
||||
"rlang",
|
||||
"stringi",
|
||||
"vctrs"
|
||||
]
|
||||
},
|
||||
"sys": {
|
||||
"Package": "sys",
|
||||
"Version": "3.4.1",
|
||||
"Source": "Repository",
|
||||
"Repository": "CRAN",
|
||||
"Hash": "34c16f1ef796057bfa06d3f4ff818a5d",
|
||||
"Requirements": []
|
||||
},
|
||||
"tinytex": {
|
||||
"Package": "tinytex",
|
||||
"Version": "0.43",
|
||||
"Source": "Repository",
|
||||
"Repository": "CRAN",
|
||||
"Hash": "facc02f3d63ed7dd765513c004c394ce",
|
||||
"Requirements": [
|
||||
"xfun"
|
||||
]
|
||||
},
|
||||
"vctrs": {
|
||||
"Package": "vctrs",
|
||||
"Version": "0.5.1",
|
||||
"Source": "Repository",
|
||||
"Repository": "CRAN",
|
||||
"Hash": "970324f6572b4fd81db507b5d4062cb0",
|
||||
"Requirements": [
|
||||
"cli",
|
||||
"glue",
|
||||
"lifecycle",
|
||||
"rlang"
|
||||
]
|
||||
},
|
||||
"xfun": {
|
||||
"Package": "xfun",
|
||||
"Version": "0.36",
|
||||
"Source": "Repository",
|
||||
"Repository": "CRAN",
|
||||
"Hash": "f5baec54606751aa53ac9c0e05848ed6",
|
||||
"Requirements": []
|
||||
},
|
||||
"yaml": {
|
||||
"Package": "yaml",
|
||||
"Version": "2.3.6",
|
||||
"Source": "Repository",
|
||||
"Repository": "CRAN",
|
||||
"Hash": "9b570515751dcbae610f29885e025b41",
|
||||
"Requirements": []
|
||||
}
|
||||
}
|
||||
}
|
||||
6
renv/.gitignore
vendored
Normal file
6
renv/.gitignore
vendored
Normal file
@ -0,0 +1,6 @@
|
||||
library/
|
||||
local/
|
||||
cellar/
|
||||
lock/
|
||||
python/
|
||||
staging/
|
||||
942
renv/activate.R
Normal file
942
renv/activate.R
Normal file
@ -0,0 +1,942 @@
|
||||
|
||||
local({
|
||||
|
||||
# the requested version of renv
|
||||
version <- "0.15.5"
|
||||
|
||||
# the project directory
|
||||
project <- getwd()
|
||||
|
||||
# figure out whether the autoloader is enabled
|
||||
enabled <- local({
|
||||
|
||||
# first, check config option
|
||||
override <- getOption("renv.config.autoloader.enabled")
|
||||
if (!is.null(override))
|
||||
return(override)
|
||||
|
||||
# next, check environment variables
|
||||
# TODO: prefer using the configuration one in the future
|
||||
envvars <- c(
|
||||
"RENV_CONFIG_AUTOLOADER_ENABLED",
|
||||
"RENV_AUTOLOADER_ENABLED",
|
||||
"RENV_ACTIVATE_PROJECT"
|
||||
)
|
||||
|
||||
for (envvar in envvars) {
|
||||
envval <- Sys.getenv(envvar, unset = NA)
|
||||
if (!is.na(envval))
|
||||
return(tolower(envval) %in% c("true", "t", "1"))
|
||||
}
|
||||
|
||||
# enable by default
|
||||
TRUE
|
||||
|
||||
})
|
||||
|
||||
if (!enabled)
|
||||
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
|
||||
112
styles.css
Normal file
112
styles.css
Normal file
@ -0,0 +1,112 @@
|
||||
|
||||
@import url('https://fonts.googleapis.com/css?family=Inter');
|
||||
@import url('https://fonts.googleapis.com/css?family=Roboto+Mono');
|
||||
|
||||
body {
|
||||
background-color: #10151A;
|
||||
background-position: center top;
|
||||
background-size: 300px 117px;
|
||||
padding-left: 10%;
|
||||
padding-right: 10%;
|
||||
color: #C4CDD5;
|
||||
font-size: 18px;
|
||||
font-weight: 400;
|
||||
font-family: Inter;
|
||||
margin-top: 10px;
|
||||
}
|
||||
|
||||
hr {
|
||||
width: 85%;
|
||||
color: #C4CDD5;
|
||||
}
|
||||
|
||||
.tocify {
|
||||
background-color: #10151A;
|
||||
font-size: 14px;
|
||||
color: #C4CDD5;
|
||||
border: 0;
|
||||
}
|
||||
|
||||
.list-group-item.active, .list-group-item.active:focus, .list-group-item.active:hover {
|
||||
background-color: #FF5517;
|
||||
border-color: #FF5517;
|
||||
}
|
||||
|
||||
.list-group-item {
|
||||
background-color: #10151A;
|
||||
}
|
||||
|
||||
h1 {
|
||||
font-size: 1.4em;
|
||||
padding-top: 10px;
|
||||
color: #FF5517;
|
||||
}
|
||||
|
||||
h2 {
|
||||
font-size: 1.1em;
|
||||
padding-top: 10px;
|
||||
color: #03FFFF;
|
||||
}
|
||||
|
||||
h3 {
|
||||
font-size: 1.1em;
|
||||
padding-top: 10px;
|
||||
color: white;
|
||||
}
|
||||
|
||||
.plotly {
|
||||
margin: 30px;
|
||||
}
|
||||
|
||||
.rt-page-button-current {
|
||||
color: #FFF;
|
||||
}
|
||||
.rt-thead {
|
||||
background-color: #10151A;
|
||||
color: #FFFFFF;
|
||||
text-align: center;
|
||||
vertical-align: middle;
|
||||
}
|
||||
|
||||
.rt-th-content {
|
||||
text-align: center;
|
||||
vertical-align: middle;
|
||||
}
|
||||
|
||||
.ReactTable {
|
||||
background-color: #171e25;
|
||||
color: #C4CDD5;
|
||||
border: none;
|
||||
font-family: Roboto Mono;
|
||||
font-size: 0.8em;
|
||||
}
|
||||
|
||||
.rt-th {
|
||||
border: 0px solid #000000 !important;
|
||||
padding-top: 15px;
|
||||
padding-bottom: 15px;
|
||||
font-weight: 400;
|
||||
font-family: Inter;
|
||||
}
|
||||
.rt-tr {
|
||||
padding-top: 5px;
|
||||
padding-bottom: 5px;
|
||||
}
|
||||
.rt-pagination {
|
||||
margin: 0;
|
||||
background: #171e25;
|
||||
opacity: 0.5;
|
||||
border-bottom: 1px solid #C4CDD5;
|
||||
border-top: 1px solid #C4CDD5;
|
||||
}
|
||||
|
||||
.btn {
|
||||
color: #FFF;
|
||||
background: none;
|
||||
border: none;
|
||||
padding: 0;
|
||||
}
|
||||
|
||||
#TOC {
|
||||
margin: 71px 0px 20px 0px;
|
||||
}
|
||||
Loading…
Reference in New Issue
Block a user