initial commit
This commit is contained in:
commit
0c791fb618
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.Rproj.user
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.Rhistory
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.RData
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.Ruserdata
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@ -0,0 +1,16 @@
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Version: 1.0
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|
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RestoreWorkspace: Default
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||||
SaveWorkspace: Default
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||||
AlwaysSaveHistory: Default
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||||
|
||||
EnableCodeIndexing: Yes
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||||
UseSpacesForTab: Yes
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||||
NumSpacesForTab: 2
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||||
Encoding: UTF-8
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||||
|
||||
RnwWeave: Sweave
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||||
LaTeX: XeLaTeX
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||||
|
||||
AutoAppendNewline: Yes
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||||
StripTrailingWhitespace: Yes
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---
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title: "Analysis of matrix spec bias-rumors"
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author: "MTRNord"
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output: pdf_document
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---
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||||
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```{r setup, echo=FALSE, message=FALSE, warning=FALSE}
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# Set so that long lines in R will be wrapped:
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knitr::opts_chunk$set(tidy.opts = list(width.cutoff = 60), tidy = TRUE)
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```
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The following data is based purely on public knowledge. This means data is fetched from github and gitlab as best as I was able to.
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# Fetching the MSCs
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||||
```{r message=FALSE, warning=FALSE, dpi=300}
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library(gh)
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library(tidyverse)
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library(nplyr)
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|
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# Set theme
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theme_set(theme_bw())
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|
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# gh_whoami()
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# Fetch all issues that are a proposal
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if (!exists("issues_all")) {
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issues_raw <- gh(
|
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"GET /repos/matrix-org/matrix-spec-proposals/issues", sort = "created",
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state = "all", direction = "asc", labels = "proposal"
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)
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issues <- as.data.frame(do.call(rbind, issues_raw))
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data <- list()
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data[[1]] <- issues
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|
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# Paginate API
|
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while (TRUE) {
|
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issues_raw <- try(
|
||||
{
|
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gh_next(issues_raw)
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}, silent = TRUE
|
||||
)
|
||||
if (inherits(issues_raw, "try-error")) {
|
||||
break
|
||||
} else {
|
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temp <- as.data.frame(do.call(rbind, issues_raw))
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data[[length(data) + 1]] <- temp
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}
|
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}
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issues_all <- do.call(rbind, data)
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}
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|
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# Filter out corrupt issues without labels
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filtered_issues <- issues_all |>
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filter(
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sapply(labels, length, simplify = TRUE) > 0
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) |>
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rowwise()
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filtered_issues$labels <- map(filtered_issues$labels, ~do.call(rbind, .))
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```
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|
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# Get Employee association from Github and Gitlab
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|
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Please note that in the current PDF this is not yet hooked up to gitlab or checking the github workplace field. It may also exclude some users that are not detectable.
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|
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```{r message=FALSE, warning=FALSE, dpi=300}
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# TODO also check against gitlab
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# TODO also check workplace thingy
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# Compile a list of who is who
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element_employee <- list()
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famedly_employee <- list()
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beeper_employee <- list()
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users <- list()
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# Get orgs of users on github
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for (i in 1:nrow(filtered_issues)) {
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user <- filtered_issues[i, ]$user[[1]]$login
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if (user %in% users) {
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next
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}
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orgs_raw <- gh(sprintf("GET /users/%s/orgs", user))
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orgs <- as.data.frame(do.call(rbind, orgs_raw))
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|
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if ("vector-im" %in% orgs$login) {
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element_employee[[length(element_employee) + 1]] <- user
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} else if ("beeper" %in% orgs$login) {
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beeper_employee[[length(beeper_employee) + 1]] <- user
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} else if ("Famedly" %in% orgs$login) {
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famedly_employee[[length(famedly_employee) + 1]] <- user
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}
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users[[length(users) + 1]] <- user
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|
||||
}
|
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```
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|
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# MSCs by Company (all kind)
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|
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Note that this does not adjust for private vs company MSCs.
|
||||
|
||||
```{r message=FALSE, warning=FALSE, dpi=300}
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|
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# Filter MSCs by company
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merged_element <- filtered_issues |>
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filter(user$login %in% element_employee) |>
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nrow()
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|
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|
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merged_famedly <- filtered_issues |>
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filter(user$login %in% famedly_employee) |>
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nrow()
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|
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merged_beeper <- filtered_issues |>
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filter(user$login %in% beeper_employee) |>
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nrow()
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|
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merged_other <- filtered_issues |>
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filter(!(user$login %in% element_employee)) |>
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filter(!(user$login %in% famedly_employee)) |>
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filter(!(user$login %in% beeper_employee)) |>
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nrow()
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|
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# Display Data
|
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data <- data.frame(
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group = c("Element", "Beeper", "Famedly", "Other"),
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value = c(merged_element, merged_beeper, merged_famedly, merged_other)
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)
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|
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# Compute the position of labels
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data <- data |>
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filter(value != 0) |>
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arrange(desc(group)) |>
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mutate(
|
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prop = value/sum(data$value) *
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100
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) |>
|
||||
mutate(
|
||||
ypos = cumsum(prop) -
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0.5 * prop
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||||
)
|
||||
|
||||
|
||||
# Basic piechart
|
||||
ggplot(data, aes(x = "", y = prop, fill = group)) +
|
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geom_bar(stat = "identity", width = 1, color = "white") +
|
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coord_polar("y", start = 0) +
|
||||
theme_void() + labs(
|
||||
title = str_wrap("Percentage of MSCs by Contributors associated with companies", 40),
|
||||
subtitle = str_wrap(
|
||||
"Note that people may have gotten mixed or people with multiple hats may have MSCs landing in the wrong category",
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||||
60
|
||||
),
|
||||
caption = "source: Github API"
|
||||
) +
|
||||
theme(legend.position = "none") +
|
||||
geom_text(
|
||||
aes(y = ypos, label = group),
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||||
color = "white", size = 5
|
||||
) +
|
||||
scale_fill_brewer(palette = "Set1")
|
||||
```
|
||||
|
||||
# Merged MSCs by Company
|
||||
|
||||
Note that this does not adjust for private vs company MSCs.
|
||||
|
||||
```{r message=FALSE, warning=FALSE, dpi=300}
|
||||
|
||||
# Filter for only merged MSCs
|
||||
merged_mscs <- filtered_issues |>
|
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filter("proposal" %in% labels) |>
|
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filter(("disposition-merge" %in% labels) | ("merged" %in% labels))
|
||||
|
||||
# Filter MSCs by company
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||||
merged_element <- merged_mscs |>
|
||||
filter(user$login %in% element_employee) |>
|
||||
nrow()
|
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|
||||
|
||||
merged_famedly <- merged_mscs |>
|
||||
filter(user$login %in% famedly_employee) |>
|
||||
nrow()
|
||||
|
||||
merged_beeper <- merged_mscs |>
|
||||
filter(user$login %in% beeper_employee) |>
|
||||
nrow()
|
||||
|
||||
merged_other <- merged_mscs |>
|
||||
filter(!(user$login %in% element_employee)) |>
|
||||
filter(!(user$login %in% famedly_employee)) |>
|
||||
filter(!(user$login %in% beeper_employee)) |>
|
||||
nrow()
|
||||
|
||||
# Display Data
|
||||
data <- data.frame(
|
||||
group = c("Element", "Beeper", "Famedly", "Other"),
|
||||
value = c(merged_element, merged_beeper, merged_famedly, merged_other)
|
||||
)
|
||||
|
||||
# Compute the position of labels
|
||||
data <- data |>
|
||||
filter(value != 0) |>
|
||||
arrange(desc(group)) |>
|
||||
mutate(
|
||||
prop = value/sum(data$value) *
|
||||
100
|
||||
) |>
|
||||
mutate(
|
||||
ypos = cumsum(prop) -
|
||||
0.5 * prop
|
||||
)
|
||||
|
||||
|
||||
# Basic piechart
|
||||
ggplot(data, aes(x = "", y = prop, fill = group)) +
|
||||
geom_bar(stat = "identity", width = 1, color = "white") +
|
||||
coord_polar("y", start = 0) +
|
||||
theme_void() + labs(
|
||||
title = str_wrap("Percentage of merged MSCs by Contributors associated with companies", 40),
|
||||
subtitle = str_wrap(
|
||||
"Note that people may have gotten mixed or people with multiple hats may have MSCs landing in the wrong category",
|
||||
60
|
||||
),
|
||||
caption = "source: Github API"
|
||||
) +
|
||||
theme(legend.position = "none") +
|
||||
geom_text(
|
||||
aes(y = ypos, label = group),
|
||||
color = "white", size = 5
|
||||
) +
|
||||
scale_fill_brewer(palette = "Set1")
|
||||
```
|
||||
|
||||
File diff suppressed because one or more lines are too long
|
|
@ -0,0 +1,21 @@
|
|||
{
|
||||
"R": {
|
||||
"Version": "4.1.2",
|
||||
"Repositories": [
|
||||
{
|
||||
"Name": "CRAN",
|
||||
"URL": "https://cran.rstudio.com"
|
||||
}
|
||||
]
|
||||
},
|
||||
"Packages": {
|
||||
"renv": {
|
||||
"Package": "renv",
|
||||
"Version": "0.16.0",
|
||||
"Source": "Repository",
|
||||
"Repository": "CRAN",
|
||||
"Hash": "c9e8442ab69bc21c9697ecf856c1e6c7",
|
||||
"Requirements": []
|
||||
}
|
||||
}
|
||||
}
|
||||
|
|
@ -0,0 +1,7 @@
|
|||
library/
|
||||
local/
|
||||
cellar/
|
||||
lock/
|
||||
python/
|
||||
sandbox/
|
||||
staging/
|
||||
|
|
@ -0,0 +1,994 @@
|
|||
|
||||
local({
|
||||
|
||||
# the requested version of renv
|
||||
version <- "0.16.0"
|
||||
|
||||
# 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"
|
||||
|
||||
args <- list(
|
||||
url = url,
|
||||
destfile = destfile,
|
||||
mode = mode,
|
||||
quiet = TRUE
|
||||
)
|
||||
|
||||
if ("headers" %in% names(formals(utils::download.file)))
|
||||
args$headers <- renv_bootstrap_download_custom_headers(url)
|
||||
|
||||
do.call(utils::download.file, args)
|
||||
|
||||
}
|
||||
|
||||
renv_bootstrap_download_custom_headers <- function(url) {
|
||||
|
||||
headers <- getOption("renv.download.headers")
|
||||
if (is.null(headers))
|
||||
return(character())
|
||||
|
||||
if (!is.function(headers))
|
||||
stopf("'renv.download.headers' is not a function")
|
||||
|
||||
headers <- headers(url)
|
||||
if (length(headers) == 0L)
|
||||
return(character())
|
||||
|
||||
if (is.list(headers))
|
||||
headers <- unlist(headers, recursive = FALSE, use.names = TRUE)
|
||||
|
||||
ok <-
|
||||
is.character(headers) &&
|
||||
is.character(names(headers)) &&
|
||||
all(nzchar(names(headers)))
|
||||
|
||||
if (!ok)
|
||||
stop("invocation of 'renv.download.headers' did not return a named character vector")
|
||||
|
||||
headers
|
||||
|
||||
}
|
||||
|
||||
renv_bootstrap_download_cran_latest <- function(version) {
|
||||
|
||||
spec <- renv_bootstrap_download_cran_latest_find(version)
|
||||
type <- spec$type
|
||||
repos <- spec$repos
|
||||
|
||||
message("* Downloading renv ", version, " ... ", appendLF = FALSE)
|
||||
|
||||
baseurl <- utils::contrib.url(repos = repos, type = type)
|
||||
ext <- if (identical(type, "source"))
|
||||
".tar.gz"
|
||||
else if (Sys.info()[["sysname"]] == "Windows")
|
||||
".zip"
|
||||
else
|
||||
".tgz"
|
||||
name <- sprintf("renv_%s%s", version, ext)
|
||||
url <- paste(baseurl, name, sep = "/")
|
||||
|
||||
destfile <- file.path(tempdir(), name)
|
||||
status <- tryCatch(
|
||||
renv_bootstrap_download_impl(url, destfile),
|
||||
condition = identity
|
||||
)
|
||||
|
||||
if (inherits(status, "condition")) {
|
||||
message("FAILED")
|
||||
return(FALSE)
|
||||
}
|
||||
|
||||
# report success and return
|
||||
message("OK (downloaded ", type, ")")
|
||||
destfile
|
||||
|
||||
}
|
||||
|
||||
renv_bootstrap_download_cran_latest_find <- function(version) {
|
||||
|
||||
# check whether binaries are supported on this system
|
||||
binary <-
|
||||
getOption("renv.bootstrap.binary", default = TRUE) &&
|
||||
!identical(.Platform$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, project = project)
|
||||
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) {
|
||||
|
||||
# if jsonlite is loaded, use that instead
|
||||
if ("jsonlite" %in% loadedNamespaces())
|
||||
renv_json_read_jsonlite(file, text)
|
||||
else
|
||||
renv_json_read_default(file, text)
|
||||
|
||||
}
|
||||
|
||||
renv_json_read_jsonlite <- function(file = NULL, text = NULL) {
|
||||
text <- paste(text %||% read(file), collapse = "\n")
|
||||
jsonlite::fromJSON(txt = text, simplifyVector = FALSE)
|
||||
}
|
||||
|
||||
renv_json_read_default <- function(file = NULL, text = NULL) {
|
||||
|
||||
# find strings in the JSON
|
||||
text <- paste(text %||% read(file), collapse = "\n")
|
||||
pattern <- '["](?:(?:\\\\.)|(?:[^"\\\\]))*?["]'
|
||||
locs <- gregexpr(pattern, text, perl = TRUE)[[1]]
|
||||
|
||||
# if any are found, replace them with placeholders
|
||||
replaced <- text
|
||||
strings <- character()
|
||||
replacements <- character()
|
||||
|
||||
if (!identical(c(locs), -1L)) {
|
||||
|
||||
# get the string values
|
||||
starts <- locs
|
||||
ends <- locs + attr(locs, "match.length") - 1L
|
||||
strings <- substring(text, starts, ends)
|
||||
|
||||
# only keep those requiring escaping
|
||||
strings <- grep("[[\\]{}:]", strings, perl = TRUE, value = TRUE)
|
||||
|
||||
# compute replacements
|
||||
replacements <- sprintf('"\032%i\032"', seq_along(strings))
|
||||
|
||||
# replace the strings
|
||||
mapply(function(string, replacement) {
|
||||
replaced <<- sub(string, replacement, replaced, fixed = TRUE)
|
||||
}, strings, replacements)
|
||||
|
||||
}
|
||||
|
||||
# transform the JSON into something the R parser understands
|
||||
transformed <- replaced
|
||||
transformed <- gsub("{}", "`names<-`(list(), character())", transformed, fixed = TRUE)
|
||||
transformed <- gsub("[[{]", "list(", transformed, perl = TRUE)
|
||||
transformed <- gsub("[]}]", ")", transformed, perl = TRUE)
|
||||
transformed <- gsub(":", "=", transformed, fixed = TRUE)
|
||||
text <- paste(transformed, collapse = "\n")
|
||||
|
||||
# parse it
|
||||
json <- parse(text = text, keep.source = FALSE, srcfile = NULL)[[1L]]
|
||||
|
||||
# construct map between source strings, replaced strings
|
||||
map <- as.character(parse(text = strings))
|
||||
names(map) <- as.character(parse(text = replacements))
|
||||
|
||||
# convert to list
|
||||
map <- as.list(map)
|
||||
|
||||
# remap strings in object
|
||||
remapped <- renv_json_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)
|
||||
|
||||
})
|
||||
|
|
@ -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
|
||||
Loading…
Reference in New Issue