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Refining system requirements #523

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2 changes: 1 addition & 1 deletion DESCRIPTION
Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
Package: pak
Version: 0.5.1.9000
Version: 0.5.1.9009
Title: Another Approach to Package Installation
Description: The goal of 'pak' is to make package installation faster and
more reliable. In particular, it performs all HTTP operations in parallel,
Expand Down
153 changes: 128 additions & 25 deletions R/system-requirements.R
Original file line number Diff line number Diff line change
@@ -1,5 +1,6 @@
DEFAULT_RSPM_REPO_ID <- "1" # cran
DEFAULT_RSPM <- "https://packagemanager.rstudio.com"
DEFAULT_REQ_URL_EXT <- ""

#' Query system requirements
#'
Expand Down Expand Up @@ -56,12 +57,119 @@ pkg_system_requirements <- function(package, os = NULL, os_release = NULL, execu
if (execute) invisible(res) else res
}

filter_repos <- function(rspm_repo_url) {
res <- curl::curl_fetch_memory(rspm_repo_url)
data <-
jsonlite::fromJSON(rawToChar(res$content), simplifyVector = FALSE)
repos <- list()
for (i in 1:length(data)) {
if ((data[[i]]$type == "R") && !data[[i]]$hidden) {
packages=as.data.frame(
available.packages(
repos=paste(DEFAULT_RSPM,data[[i]]$name,"latest",sep="/")
)
)$Package
message(paste(DEFAULT_RSPM,data[[i]]$name,"latest",sep="/"))
repos[[length(repos)+1]]=list(id=data[[i]]$id, packages=packages)
}
if ((data[[i]]$type == "Bioconductor") && (data[[i]]$name != "all") && !data[[i]]$hidden) {
Sys.setenv(BioC_mirror=paste(DEFAULT_RSPM,data[[i]]$name,sep="/"))
bioc_repos<-BiocManager::repositories()
bioc_repos[names(bioc_repos)[grep("BioC",names(bioc_repos),invert=TRUE)]]<-""
packages=as.data.frame(available.packages(repos=bioc_repos))$Package
repos[[length(repos)+1]]=list(id=data[[i]]$id, packages=packages)
}


}
repos
}


find_package_deps <- function(rspm_repo_url,
package,
os,
os_release,
repos) {
appendstr <- ""
repo_ctr = 1
deps<-c()
deps_found <- FALSE
message(sprintf("%s: length_repos %s", repo_ctr, length(repos)))
if (!is.null(package)) {
while (repo_ctr<=length(repos)) {
packages_in_repo <-
repos[[repo_ctr]]$packages[repos[[repo_ctr]]$packages %in% package]
message(sprintf("%s: length %s", repo_ctr, length(packages_in_repo)))
message(repo_ctr, packages_in_repo)

if (length(packages_in_repo) == 0) {
message(paste("none of ", package, "found in repo", repo_ctr))
repo_ctr <- repo_ctr + 1
} else {
deps_found <- FALSE
while (!deps_found) {
message(sprintf(">>> %s", repo_ctr))
req_url <- sprintf(
"%s/%s/sysreqs?all=false&pkgname=%s&distribution=%s&release=%s%s",
rspm_repo_url,
repos[[repo_ctr]]$id,
paste(packages_in_repo, collapse = "&pkgname="),
os,
os_release,
appendstr
)
message(sprintf("%s: %s", repo_ctr, req_url))
res <- curl::curl_fetch_memory(req_url)
message(sprintf("A %s: %s", repo_ctr, res$status_code))
if (res$status_code == "404" &&
length(res$content) == 0) {
repo_ctr = repo_ctr + 1
message(sprintf("B %s: %s", repo_ctr, res$status_code))
} else {
data <-
jsonlite::fromJSON(rawToChar(res$content), simplifyVector = FALSE)
message(sprintf("C %s: %s", repo_ctr, data$error))
if (!is.null(data$error) &&
data$error == sprintf("Could not locate package '%s'", "test")) {
repo_ctr <- repo_ctr + 1
}
appendstr <- ""
if (!is.null(data$error) &&
data$error == "Bioconductor version not provided") {
if (!exists("biocvers")) {
biocvers <- BiocManager::version()
}
appendstr = sprintf("&bioc_version=%s", biocvers)
}
if (res$status_code == "200") {
deps_found <- TRUE
repo_ctr <- repo_ctr + 1
data
deps=c(deps,data$requirements)
message(rawToChar(res$content))
}

}

}

}

}
deps
}
}


system_requirements_internal <- function(os, os_release, root, package, execute, sudo, echo) {
if (is.null(os) || is.null(os_release)) {
d <- distro::distro()
os <- os %||% d$id
os_release <- os_release %||% d$short_version
}



os_versions <- supported_os_versions()

Expand All @@ -71,28 +179,16 @@ system_requirements_internal <- function(os, os_release, root, package, execute,

rspm <- Sys.getenv("RSPM_ROOT", DEFAULT_RSPM)
rspm_repo_id <- Sys.getenv("RSPM_REPO_ID", DEFAULT_RSPM_REPO_ID)
rspm_repo_url <- sprintf("%s/__api__/repos/%s", rspm, rspm_repo_id)
rspm_repo_url <- sprintf("%s/__api__/repos", rspm)


if (!is.null(package)) {
req_url <- sprintf(
"%s/sysreqs?all=false&pkgname=%s&distribution=%s&release=%s",
rspm_repo_url,
paste(package, collapse = "&pkgname="),
os,
os_release
)
res <- curl::curl_fetch_memory(req_url)
data <- jsonlite::fromJSON(rawToChar(res$content), simplifyVector = FALSE)
if (!is.null(data$error)) {
stop(data$error)
}

data<-find_package_deps(rspm_repo_url,package,os,os_release,filter_repos(rspm_repo_url))

pre_install <- unique(unlist(c(data[["pre_install"]], lapply(data[["requirements"]], `[[`, c("requirements", "pre_install")))))
install_scripts <- unique(unlist(c(data[["install_scripts"]], lapply(data[["requirements"]], `[[`, c("requirements", "install_scripts")))))
}

else {
pre_install <- unique(unlist(c(data[["pre_install"]], lapply(data, `[[`, c("requirements", "pre_install")))))
install_scripts <- unique(unlist(c(data[["install_scripts"]], lapply(data, `[[`, c("requirements", "install_scripts")))))
} else {
desc_file <- normalizePath(file.path(root, "DESCRIPTION"), mustWork = FALSE)
if (!file.exists(desc_file)) {
stop("`", root, "` must contain a package.", call. = FALSE)
Expand Down Expand Up @@ -169,13 +265,20 @@ supported_os_versions <- function() {
# Grouping multiple `apt-get install -y` calls in install scripts.
# This should be done by the server, but isn't (yet).
simplify_install <- function(x) {
rx <- "^apt-get install -y ([a-z0-9-]+)$"
if (length(x) == 0 || !all(grepl(rx, x))) {
rx <- "^apt-get install -y"
ry <- "^yum install -y"
if (length(x) == 0 ||
(!all(grepl(rx, x)) && !all(grepl(ry, x)))) {
return(x)
}

paste0(
"apt-get install -y ",
paste(gsub(rx, "\\1", x), collapse = " ")
)

if (all(grepl(rx, x))) {
return(paste0("apt-get install -y ",
paste(gsub(rx, "", x), collapse = " ")))
}

if (all(grepl(ry, x))) {
return(paste0("yum install -y ",
paste(gsub(ry, "", x), collapse = " ")))
}
}