Skip to content

added passthrough options #199

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
merged 2 commits into from
Nov 19, 2020
Merged

added passthrough options #199

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
4351b08
added passthrough options
muschellij2 Oct 23, 2020
f6352cf
too many arguments copied over
muschellij2 Oct 23, 2020
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
200 changes: 169 additions & 31 deletions R/debian.R
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -2,6 +2,12 @@
#'
#' @param droplet A droplet, or object that can be coerced to a droplet
#' by \code{\link{as.droplet}}.
#' @param user User name. Defaults to "root".
#' @param keyfile Optional private key file.
#' @param ssh_passwd Optional passphrase or callback function for authentication.
#' Refer to the \code{ssh::ssh_connect} documentation for more
#' details.
#' @param verbose If TRUE, will print command before executing it.
#' @name debian
#' @examples
#' \dontrun{
Expand All @@ -21,22 +27,46 @@ NULL

#' @rdname debian
#' @export
debian_add_swap <- function(droplet) {
debian_add_swap <- function(droplet,
user = "root",
keyfile = NULL,
ssh_passwd = NULL,
verbose = FALSE
) {
droplet_ssh(droplet,
"fallocate -l 4G /swapfile",
"chmod 600 /swapfile",
"mkswap /swapfile",
"sudo swapon /swapfile",
"sudo echo \"/swapfile none swap sw 0 0\" >> /etc/fstab"
"sudo echo \"/swapfile none swap sw 0 0\" >> /etc/fstab",
user = user,
keyfile = keyfile,
ssh_passwd = ssh_passwd,
verbose = verbose
)
}

#' @rdname debian
#' @export
debian_install_r <- function(droplet) {
debian_install_r <- function(droplet,
user = "root",
keyfile = NULL,
ssh_passwd = NULL,
verbose = FALSE
) {
droplet %>%
debian_apt_get_install("r-base", "r-base-dev") %>%
droplet_ssh('echo "options(repos=c(\'http://cran.rstudio.com/\'))" > .Rprofile')
debian_apt_get_install("r-base", "r-base-dev",
user = user,
keyfile = keyfile,
ssh_passwd = ssh_passwd,
verbose = verbose
) %>%
droplet_ssh('echo "options(repos=c(\'http://cran.rstudio.com/\'))" > .Rprofile',
user = user,
keyfile = keyfile,
ssh_passwd = ssh_passwd,
verbose = verbose
)
}

#' @rdname debian
Expand All @@ -45,58 +75,125 @@ debian_install_r <- function(droplet) {
#' @param version Version of rstudio to install.
#' @export
debian_install_rstudio <- function(droplet, user = "rstudio", password = "server",
version = "0.99.484") {
version = "0.99.484",
keyfile = NULL,
ssh_passwd = NULL,
verbose = FALSE
) {
droplet %>%
debian_apt_get_install("gdebi-core", "libapparmor1") %>%
debian_apt_get_install("gdebi-core", "libapparmor1",
user = user,
keyfile = keyfile,
ssh_passwd = ssh_passwd,
verbose = verbose
) %>%
droplet_ssh(
sprintf('wget http://download2.rstudio.org/rstudio-server-%s-amd64.deb', version),
sprintf("sudo gdebi rstudio-server-%s-amd64.deb --non-interactive", version),
sprintf('adduser %s --disabled-password --gecos ""', user),
sprintf('echo "%s:%s" | chpasswd', user, password)
sprintf('echo "%s:%s" | chpasswd', user, password),
user = user,
keyfile = keyfile,
ssh_passwd = ssh_passwd,
verbose = verbose
)
}

#' @rdname debian
#' @export
debian_install_shiny <- function(droplet, version = "1.4.0.756") {
debian_install_shiny <- function(droplet, version = "1.4.0.756",
user = "root",
keyfile = NULL,
ssh_passwd = NULL,
verbose = FALSE
) {
droplet %>%
debian_install_r() %>%
install_r_package("shiny") %>%
install_r_package("rmarkdown") %>%
debian_apt_get_install("gdebi-core") %>%
debian_install_r(
user = user,
keyfile = keyfile,
ssh_passwd = ssh_passwd,
verbose = verbose
) %>%
install_r_package("shiny",
user = user,
keyfile = keyfile,
ssh_passwd = ssh_passwd,
verbose = verbose
) %>%
install_r_package("rmarkdown",
user = user,
keyfile = keyfile,
ssh_passwd = ssh_passwd,
verbose = verbose
) %>%
debian_apt_get_install("gdebi-core",
user = user,
keyfile = keyfile,
ssh_passwd = ssh_passwd,
verbose = verbose
) %>%
droplet_ssh(
sprintf("wget http://download3.rstudio.org/ubuntu-12.04/x86_64/shiny-server-%s-amd64.deb", version),
sprintf("sudo gdebi shiny-server-%s-amd64.deb --non-interactive", version)
sprintf("sudo gdebi shiny-server-%s-amd64.deb --non-interactive", version),
user = user,
keyfile = keyfile,
ssh_passwd = ssh_passwd,
verbose = verbose
)
}

debian_install_opencpu <- function(droplet, version = "1.5") {
debian_install_opencpu <- function(droplet, version = "1.5",
user = "root",
keyfile = NULL,
ssh_passwd = NULL,
verbose = FALSE
) {
droplet %>%
droplet_ssh(
paste0("sudo add-apt-repository ppa:opencpu/opencpu-", version),
"sudo apt-get update",
"sudo apt-get -q -y install opencpu",
"sudo service opencpu start"
"sudo service opencpu start",
user = user,
keyfile = keyfile,
ssh_passwd = ssh_passwd,
verbose = verbose
)
}

# apt-get helpers --------------------------------------------------------------

#' @rdname debian
#' @export
debian_apt_get_update <- function(droplet) {
debian_apt_get_update <- function(droplet,
user = "root",
keyfile = NULL,
ssh_passwd = NULL,
verbose = FALSE) {
droplet_ssh(droplet,
"sudo apt-get update -qq",
"sudo apt-get upgrade -y"
"sudo apt-get upgrade -y",
user = user,
keyfile = keyfile,
ssh_passwd = ssh_passwd,
verbose = verbose
)
}

#' @rdname debian
#' @export
#' @param ... Arguments to apt-get install.
debian_apt_get_install <- function(droplet, ...) {
debian_apt_get_install <- function(droplet, ...,
user = "root",
keyfile = NULL,
ssh_passwd = NULL,
verbose = FALSE) {
droplet_ssh(droplet,
paste0("sudo apt-get install -y --force-yes ", paste(..., collapse = " "))
paste0("sudo apt-get install -y --force-yes ", paste(..., collapse = " ")),
user = user,
keyfile = keyfile,
ssh_passwd = ssh_passwd,
verbose = verbose
)
}

Expand All @@ -106,17 +203,33 @@ debian_apt_get_install <- function(droplet, ...) {
#' @export
#' @param package Name of R package to install.
#' @param repo CRAN mirror to use.
install_r_package <- function(droplet, package, repo = "https://cloud.r-project.org/") {
install_r_package <- function(droplet, package, repo = "https://cloud.r-project.org/",
user = "root",
keyfile = NULL,
ssh_passwd = NULL,
verbose = FALSE
) {
droplet_ssh(droplet,
sprintf("Rscript -e \"install.packages(\'%s\', repos=\'%s/\')\"", package, repo)
sprintf("Rscript -e \"install.packages(\'%s\', repos=\'%s/\')\"",
package, repo),
user = user,
keyfile = keyfile,
ssh_passwd = ssh_passwd,
verbose = verbose
)
}

#' @rdname debian
#' @export
#' @param package Name of R package to install.
#' @param repo CRAN mirror to use.
install_github_r_package <- function(droplet, package, repo = "https://cloud.r-project.org/") {
install_github_r_package <- function(droplet, package,
repo = "https://cloud.r-project.org/",
user = "root",
keyfile = NULL,
ssh_passwd = NULL,
verbose = FALSE
) {
tf <- tempdir()
randName <- paste(sample(c(letters, LETTERS), size = 10,
replace = TRUE), collapse = "")
Expand All @@ -127,12 +240,27 @@ install_github_r_package <- function(droplet, package, repo = "https://cloud.r-p
}
})
command = "Rscript -e \"cat(requireNamespace('remotes', quietly = TRUE))\""
droplet_ssh(droplet, paste0(command, " > /tmp/",
randName), verbose = FALSE)
droplet_download(droplet, paste0("/tmp/", randName),
tf, verbose = FALSE)
droplet_ssh(droplet,
paste0(command,
" > /tmp/",
randName),
user = user,
keyfile = keyfile,
ssh_passwd = ssh_passwd,
verbose = verbose
)
droplet_download(droplet,
paste0("/tmp/", randName),
tf,
user = user,
keyfile = keyfile,
ssh_passwd = ssh_passwd,
verbose = verbose)
droplet_ssh(droplet, paste0("rm /tmp/", randName),
verbose = FALSE)
user = user,
keyfile = keyfile,
ssh_passwd = ssh_passwd,
verbose = verbose)

have_remotes <- readLines(tff, warn = FALSE)
if (length(have_remotes) == 1) {
Expand All @@ -145,11 +273,21 @@ install_github_r_package <- function(droplet, package, repo = "https://cloud.r-p
have_remotes = FALSE
}
if (!have_remotes) {
install_r_package(droplet, "remotes", repo = repo)
install_r_package(droplet, "remotes", repo = repo,
user = user,
keyfile = keyfile,
ssh_passwd = ssh_passwd,
verbose = verbose
)
}

droplet_ssh(
droplet_ssh(
droplet,
sprintf("Rscript -e \"remotes::install_github('%s')\"",
package))
package),
user = user,
keyfile = keyfile,
ssh_passwd = ssh_passwd,
verbose = verbose
)
}
Loading