Package 'vmr'

Title: Virtual Machines for R
Description: Manage, provision and use Virtual Machines pre-configured for R. Develop, test and build package in a clean environment. 'Vagrant' tool and a provider (such as 'Virtualbox') have to be installed.
Authors: Jean-François Rey [cre, aut]
Maintainer: Jean-François Rey <[email protected]>
License: GPL (>= 3)
Version: 0.0.6
Built: 2024-11-01 06:43:07 UTC
Source: CRAN

Help Index

Virtual Machines for R

Description

Manage, provision and use Virtual Machines pre-configured for R. Develop, test and build package in a clean environment. 'Vagrant' tool and a provider (such as 'Virtualbox') have to be installed.

Details

Package: vmr
Type: Package
Version: 0.0.6
Date: 2023-03-07
License: GPL (>=3)

This package is a wrap of the Vagrant tool and more. It allows to manage, provision and use Virtual Machines pre-configured for R. It currently only uses 'Virtualbox' (>= 6.1.14) as provider. Vagrant tool have to be installed too. Used VMs come from https://app.vagrantup.com/VMR repository and the sources use to generate them can be found at https://gitlab.com/rstuff/vms. See vignettes for the documentations browseVignette("vmr").

Author(s)

Jean-François Rey [email protected]

Maintainer: Jean-François Rey [email protected]

See Also

Useful links:

Examples

## Not run: 
library("vmr")

## End(Not run)

List provider options

Description

List a provider available options.

Usage

getProviderOptions(provider = "virtualbox", details = FALSE)

Arguments

provider

a provider name
details

if TRUE print options, otherwise return default options

Details

It return a list of options name and value for a specific provider. To get the help page do ⁠?<provider_name>Options()⁠, for example [virtualboxOptions()].

Value

a list of options

Examples

vbOpts <- getProviderOptions(provider = "virtualbox")
print(vbOpts)

Print vmr object information

Description

print information from a vmr object

Usage

## S3 method for class 'vmr'
print(x, ...)

Arguments

x

a vmr object
...

optional print arguments

Value

the vmr object (via invisible(x))

Summary vmr object information

Description

print information from a vmr object

Usage

## S3 method for class 'vmr'
summary(object, ...)

Arguments

object

a vmr object
...

optional print arguments

Value

the vmr object (via invisible(x))

Configure the guest VM to be use as a Gitlab-Runner

Description

Configure the guest VM to be use as a GitLab Runner and return the command to run in shell to register it.

Usage

virtualboxGitlabRunner(
  vmr,
  gitlab_url,
  gt_token,
  snapshot_name = "",
  vm_name = ""
)

Arguments

vmr

a vmr object
gitlab_url

a GitLab URL with protocol (http or https)
gt_token

a GitLab registration token
snapshot_name

name of a snapshot to use if any
vm_name

the 'VitualBox' VM name if not specified in 'vmr' object provider_options.

Value

Character command to run in shell to register it

Examples

## Not run: 
cmd <- virtualboxGitLabRunner(vmr, "gitlab.com", "mytoken")
system(cmd)

## End(Not run)

List 'VirtualBox' options available

Description

List available options for 'VirtualBox' provider

Usage

virtualboxOptions(details = TRUE)

Arguments

details

if TRUE print options (default), otherwise only return default options

Details

Get the 'VirtualBox' default options. It return a list as follow: 

list(
gui = TRUE,
name = NULL,
nic_type = NULL,
linked_clone = FALSE,
check_guest_additions = TRUE,
modifyvm = list(cpus = "2", memory = "4096")
)

  • gui: if TRUE show the GUI, otherwise headless mode is actived

  • name: the 'VirtualBox' instance name

  • nic_type: the NIC type for the network interface to use, by default use the default one. see VirtualBox Networking

  • linked_clone: if TRUE, linked clones are based on a master VM, which is generated by importing the base box only once the first time it is required. For the linked clones only differencing disk images are created where the parent disk image belongs to the master VM. (Be careful, master VM can't be remove until linked_clone still exists)

  • check_guest_additions: If TRUE (default) check if guest have guest additions installed.

  • modifyvm: list of 'VirtualBox' properties for the guest VM (such as number of cpus, memory size,...). see 'VirtualBox' modifyvm

Value

A default list of options 

list(
gui = TRUE,
name = NULL,
nic_type = NULL,
linked_clone = FALSE,
check_guest_additions = TRUE,
modifyvm = list(cpus = "2", memory = "4096")
)

Examples

## Not run: 
vb.opts <- virtualboxOptions(details = FALSE)
vb.opts$modifyvm$cpus <- "4"
vb.opts$modifyvm$memory <- "8192"
vb.opts

## End(Not run)

Download a Box

Description

Download a box from a vmr object.

Usage

vmrBoxDownload(vmr)

Arguments

vmr

a vmr object

Value

a vmr object

Configure ssh

Description

Configure ssh credential.

Usage

vmrConfigSSH(
  vmr,
  ssh_user = "vagrant",
  ssh_pwd = "vagrant",
  port = "",
  ssh_private_key_path = ""
)

Arguments

vmr

a vmr object
ssh_user

the ssh user (default 'vagrant')
ssh_pwd

the ssh pwd if any (default 'vagrant')
port

the ssh port (default empty)
ssh_private_key_path

path to the private ssh key to use (default empty, use insecure vagrant key)

Details

by default vmr use vagrant as user/password and insecure key for ssh connection. This behavior can be change here, by setting an another user and/or ssh keys. Calling with no arguments will disable this option. Be careful, ssh using only password may result of vmr functions bugs.

Value

an updated vmr object

Examples

## Not run: 
vmr <- vmrConfigSSH(ssh_user = "John", ssh_pwd = "d0e", port = "22")
vmr <- vmrConfigSSH(ssh_user = "John", private_key_path = "/path/to/private/key/")

## End(Not run)

Open a ssh connection to guest machine

Description

Open a ssh connection to guest machine

Usage

vmrConnect(vmr)

Arguments

vmr

a vmr object

Details

To open a ssh connection 'ssh' package have to be installed.

Value

a vmr object

Create a vmr environment class

Description

Create a vmr object.

Usage

vmrCreate(
  name,
  provider = "virtualbox",
  version = "latest",
  provider.options = virtualboxOptions(FALSE)
)

Arguments

name

a box name
provider

the box provider (default: "virtualbox")
version

the box version (default : "latest")
provider.options

provider options (call [getProviderOptions()] to get values)

Details

Create a S3 vmr object (a simple list). The object contains all information needed to configure and manage a vmr environment (a vagrant environment).

A vmr environment need mostly a box name and a provider. The environment is attached to the current working directory.

vmr object main attributs:

  • path: working directory

  • org: Vagrant cloud user/organization name 'VMR'

  • box: the box name

  • version: the box version

  • provider: the provider

  • provider_options: the provider options (see [getProviderOptions()])

  • vagrantName: Vagrant environment name

  • ID <- Vagrant environment ID

  • synced_folder: a list with source and destination

  • ssh_user: the ssh user

  • ssh_pwd: the ssh user password

  • ssh_port: the ssh port

  • ssh_private_key_path: the private ssh key path

Value

a vmr object (see details)

Examples

## Not run: 
# List boxes available
boxes <- vmrList()
# Create a vmr object
vmr <- vmrCreate(boxes$Name[1])

# to customize the guest machine for virtualbox
virtualboxOpts <- getProviderOptions(provider = "virtualbox")
virtualboxOpts$modifyvm <- list(cpus = 4, memory = 4096)
virtualboxOpts$name <- "My VM Cool Name"
# To specify a provider and version
vmr <- vmrCreate(
  name = boxes$Name[1],
  provider = "virtualbox",
  version = boxes$Version[1],
  provider.options = virtualboxOpts
)

## End(Not run)

Remove all resources created in a vmr environment

Description

Remove all resources created by vmrStart()

Usage

vmrDestroy(id = "", force = FALSE)

Arguments

id

a vmr environment id (default : "" id from the current environment)
force

if TRUE force to remove

Details

Will by default remove all resources created from the current vmr environment. By specifying the id any environment with this id will be remove.

Value

the vagrant environment id

Examples

## Not run: 
vmrStop()
vmrDestroy()

## End(Not run)

Disconnect ssh connection to guest machine

Description

Close a ssh connection to the guest machine

Usage

vmrDisconnect(vmr)

Arguments

vmr

a vmr object

Details

'ssh' package need to be installed.

Value

a vmr object

Execute R methods into guest machine

Description

Run R method into guest machine.

Usage

vmrExec(cmd = c())

Arguments

cmd

list of R command

Details

call Rscript -e "cmd" into the guest machine from the current vmr environment. Command are independents and do not keep memory of past commands.

Value

NULL

Examples

## Not run: 
cmd <- c("Sys.info()", 'print("Hello World!")')
vmrExec(cmd)

## End(Not run)

Get guest machine information

Description

Get guest machine information. Print OS, R, R-devel and R packages information. Still in development.

Usage

vmrInfo()

Value

NULL

Examples

## Not run: 
boxes <- vmrList()
vmr <- vmrCreate(boxes$Name[1])
vmr <- vmrInitEnv(vmr)
vmrStart()
vmrInfo()

## End(Not run)

Initialize the vmr environment

Description

Create vmr environment in the current directory. Set configuration into a template file name "Vagrantfile" and download the box if needed.

Usage

vmrInitEnv(vmr, force.vagrantfile = FALSE, force.download = FALSE)

Arguments

vmr

a vmr object
force.vagrantfile

if TRUE force to overwrite environment configuration (default FALSE)
force.download

if TRUE force to download the box, otherwise do not (default FALSE).

Details

The vmr environment consist of a directory (the working directory) and a template file name Vagrantfile. If the box is not present in localhost it will be download.

Value

the vmr object

Examples

## Not run: 
boxes <- vmrList()
vmr <- vmrCreate(boxes$Name[1])
vmr <- vmrInitEnv(vmr)

## End(Not run)

Install R packages into guest machine

Description

Install a list of R packages into the guest machine of the current vmr environment.

Usage

vmrInstallPackages(pkgs = c())

Arguments

pkgs

list of R packages

Value

installed packages vector

Examples

## Not run: 
vmrInstallPackages(c("vmr"))

## End(Not run)

Is vmr environment running

Description

Check if a guest machine in a vmr environment is running

Usage

vmrIsRunning()

Value

TRUE if running, otherwise FALSE

Examples

## Not run: 
lboxes <- vmrList()
vmr <- vmrCreate(lboxes$Name[1])
vmr <- vmrInitEnv(vmr)
vmrStart()
vmrIsRunning()
vmrStop()
vmrIsRunning()

## End(Not run)

List available boxes from VagrantCloud

Description

List of available boxes from a VagrantCloud organization account.

Usage

vmrList(org = .VagrantCloudOrganization)

Arguments

org

Vagrant Cloud organization name (default : 'VMR')

Details

Default usage lists boxes preconfigurated with R from VMR organization account.

Value

a data.frame with Name, Provider, Version and Description of available boxes

List all available version of a box

Description

List all versions and providers available of a box.

Usage

vmrListBox(box_name, org = .VagrantCloudOrganization)

Arguments

box_name

the box name
org

Vagrant Cloud organization name (default : 'VMR')

Details

List information of a box from VagrantCloud. Default usage list information of a box preconfigurated with R from VMR organization account.

Value

a data.frame with "Name, "Version", "Description", "Provider" and "Date" of the box

Examples

## Not run: 
# List Boxes
boxes <- vmrList()
# Box informaion
box_info <- vmrListBox(boxes$Name[1])
box_info

## End(Not run)

List snapshot of the guest machine

Description

Print all snapshot name of the guest machine

Usage

vmrListSnapshot()

Value

NULL

Load a vmr environment containing a Vagrant file

Description

Load a vmr environment containing a VagrantFile and create a vmr object (see [vmrCreate()] for object details).

Usage

vmrLoad(dir = "./", vagrantfileName = "Vagrantfile")

Arguments

dir

the vmr environment directory (default: "./")
vagrantfileName

a Vagrantfile name (default: "Vagrantfile")

Details

It read a Vagrant file template with vmr compatible parameters. It's an experimental Vagrant file reading, some parameters may not be loaded.

Value

a vmr object

Examples

## Not run: 
# load the Vagrantfile in the current directory
vmr <- vmrLoad(getwd())

## End(Not run)

List downloaded boxes

Description

List all boxes downloaded in localhost

Usage

vmrLocalBoxList()

Value

a data.frame with boxes Name, Providers and Version

Examples

## Not run: 
localBoxes <- vmrLocalBoxList()
print(localBoxes)

## End(Not run)

Remove old installed boxes

Description

Removes old versions of installed boxes.

Usage

vmrLocalBoxPrune()

Value

a data.frame of still installed boxes (Name, Poviders and Version)

Examples

## Not run: 
vmrLocalBoxPrune()

## End(Not run)

Remove a box from localhost

Description

Remove a specific box from localhost.

Usage

vmrLocalBoxRemove(name, provider = "", version = "", force = FALSE)

Arguments

name

the box name
provider

the box provider (default: first provider found)
version

the box version (default: version available)
force

if TRUE force to remove

Value

execution code or message

Examples

## Not run: 
lboxes <- vmrLocalBoxList()
vmrLocalBoxRemove(lboxes$Name[[1]])
# if multiple providers and versions
vmrLocalBoxRemove(lboxes$Name[[1]], lboxes$Provider[[1]], lboxes$Version[[1]])

## End(Not run)

Update local box version

Description

Download the latest version of the box use in the current vmr environment.

Usage

vmrLocalBoxUpdate()

Value

execution code or message

Mount a host directory to guest

Description

Mount a host directory to the guest machine.

Usage

vmrMountDir(vmr, src = "", dest = "")

Arguments

vmr

a vmr object
src

a host directory
dest

a destination guest directory

Details

If the option of mounting a directory is available in the guest provider, it will mount src to destination directory. Calling with no arguments will disable this option.

Value

a vmr object

Examples

## Not run: 
boxes <- vmrList()
vmr <- vmrCreate(boxes$Name[1])
vmr <- vmrMountDir(vmr, src = getwd(), dest = "/vmr")
vmr <- vmrInitEnv(vmr)
vmrStart()

## End(Not run)

Build a package in the guest machine

Description

Build a package bundle or binary into the guest machine.

Usage

vmrPackageBuild(pkg = "./", binary = FALSE)

Arguments

pkg

a package directory or a tar.gz file
binary

if TRUE build binary package otherwise FALSE

Details

upload the package and run devtools::build() (build available in $HOME/vmr/package/pkg) in the current vmr environment.

Value

NULL

Perform a package check on guest

Description

Perform a package check into the guest

Usage

vmrPackageCheck(pkg = "./")

Arguments

pkg

a package directory or a tar.gz file

Details

upload the package and run devtools::check() into the guest machine. (check available in $HOME/vmr/package/pkg). Checking a directory with multiple files may slower upload, prefer tar.gz file

Value

NULL

Examples

## Not run: 
vmrPackageCheck("vmr_package.tar.gz")

## End(Not run)

Test a package into a guest machine

Description

Test a package into a guest machine

Usage

vmrPackageTest(pkg = "./")

Arguments

pkg

a package directory or tar.gz

Details

Perform a package check into the guest machine of the current vmr environment using devtools::test(). (tests are available in $HOME/vmr/package/pkg)

Value

NULL

Provision a vmr environment

Description

Provision a vmr environment.

Usage

vmrProvision(cmd = c(), elts = c(), dest = "")

Arguments

cmd

list of shell commands
elts

list of files and/or directories
dest

destination of elts (default HOME/vmr)

Details

Upload 'elts' files and/or directories to the guest machine 'dest' from the current vmr environment. And finaly run shell commands 'cmd' in the guest machine.

Value

NULL

remove a snapshot of the guest machine

Description

remove a snapshot of the guest machine

Usage

vmrRemoveSnapshot(snap_name)

Arguments

snap_name

the snapshot name

Value

NULL

Restore a snapshot of the guest machine

Description

Restore a snapshot of the guest machine.

Usage

vmrRestoreSnapshot(snap_name)

Arguments

snap_name

the snapshot name

Value

the snapshot name

Examples

## Not run: 
vmrRestoreSnapshot("my snapshot")

## End(Not run)

Resume a stopped guest machine

Description

Resume a stopped guest machine.

Usage

vmrResume()

Details

In the current vmr environment, start a stopped ([vmrSuspend()]) guest machine.

Value

NULL

Send files and/or directories to guest machine

Description

Send files and/or directories to the guest machine in the current vmr environment. They are upload into ~/vmr/ directory.

Usage

vmrSend(elt = c())

Arguments

elt

list of files and directories

Value

0 if OK, message otherwise

Examples

## Not run: 
vmrSend(c("myfile"))

## End(Not run)

Set verbose level

Description

Set verbose level for vmr package functions

Usage

vmrSetVerbose(verbose_mode = "Normal")

Arguments

verbose_mode

"None", "Normal" or "Full"

Details

Three verboses mode is available:

  • "None" : print nothings

  • "Normal" : print essential

  • "Full" : print all

Value

invisible verbose value

Start a vmr environment

Description

Start a guest virtual machine using the current vmr environment (directory and Vagrantfile template)

Usage

vmrStart()

Value

the vmr environment unique id

Examples

## Not run: 
lboxes <- vmrList()
vmr <- vmrCreate(lboxes$Name[1])
vmr <- vmrInitEnv(vmr)
vmrStart()
vmrStop()

## End(Not run)

Get the state of the guest machine

Description

Print guest machine state in the current vmr environment.

Usage

vmrStatus()

Value

a data.frame with Name, Provider and state

Stop a vmr environement

Description

Stop a guest virtual machine in the current vmr environment.

Usage

vmrStop(force = FALSE)

Arguments

force

if TRUE force to stop (powerOff), otherwise FALSE clean shutdown

Value

NULL

Examples

## Not run: 
lboxes <- vmrList()
vmr <- vmrCreate(lboxes$Name[1])
vmr <- vmrInitEnv(vmr)
vmrStart()
vmrStop()

## End(Not run)

Save state and stop guest machine

Description

Save the guest machine and stop it.

Usage

vmrSuspend()

Details

In the current vmr environment, save the state of the guest machine and stop it.

Value

NULL

Take a snapshot of the guest machine

Description

Take a snapshot of the guest machine.

Usage

vmrTakeSnapshot(snap_name)

Arguments

snap_name

the name given to the snapshot

Value

the snapshot name (invisible)

Examples

## Not run: 
vmrTakeSnapshot("my snapshot")

## End(Not run)

Update a vmr environment.

Description

Force to use the latest box version of the current vmr environment.

Usage

vmrUpdateEnvVersion(vmr)

Arguments

vmr

a vmr object

Details

Put vmr object version to latest and update the Vagrant File template. Download the new box version if needed.

Value

a vmr object

Examples

## Not run: 
boxes <- vmrList()
vmr <- vmrCreate(boxes$Name[1], version = "oldone")
vmr <- vmrInitEnv(vmr)

# update to latest
vmr <- vmrUpdateEnvVersion(vmr)
vmrStart()

## End(Not run)

Update R packages installed

Description

Updates R packages installed in the guest machine.

Usage

vmrUpdatePackages()

Details

Will perform a update.packages() in the guest machine of the current vmr environment.

Examples

## Not run: 
lboxes <- vmrList()
vmr <- vmrCreate(lboxes$Name[1])
vmr <- vmrInitEnv(vmr)
vmrStart()
vmrUpdatePackages()

## End(Not run)