问题
I have installed R using below line in my docker file. Please suggest how do I specify now packages to be installed in my docker file.
RUN yum -y install R-core R-devel
I'm doing something like this:
RUN R -e "install.packages('methods',dependencies=TRUE, repos='http://cran.rstudio.com/')"\
&& R -e "install.packages('jsonlite',dependencies=TRUE, repos='http://cran.rstudio.com/')" \
&& R -e "install.packages('tseries',dependencies=TRUE, repos='http://cran.rstudio.com/')"
Is this the right way to do?
回答1:
As suggested by @Cameron Kerr's comment, Rscript does not give you a build failure. As of now, the recommended way is to do as the question suggests.
RUN R -e "install.packages('methods',dependencies=TRUE, repos='http://cran.rstudio.com/')"
RUN R -e "install.packages('jsonlite',dependencies=TRUE, repos='http://cran.rstudio.com/')"
RUN R -e "install.packages('tseries',dependencies=TRUE, repos='http://cran.rstudio.com/')"
If you're fairly certain of no package failures then use this one-liner -
RUN R -e "install.packages(c('methods', 'jsonlite', 'tseries'),
dependencies=TRUE,
repos='http://cran.rstudio.com/')"
EDIT: If you're don't use the Base-R image, you can use rocker-org's r-ver or r-studio or tidyverse images. Here's the repo. Here's an example Dockerfile -
FROM rocker/tidyverse:latest
# Install R packages
RUN install2.r --error \
methods \
jsonlite \
tseries
The --error flag is optional, it makes install.packages() throw an error if the package installation fails (which will cause the docker build command to fail). By default, install.packages() only throws a warning, which means that a Dockerfile can build successfully even if it has failed to install the package.
All rocker-org's basically install the littler package for the install2.R functionality
回答2:
Yes, your solution should work. I came across the same problem and found the solution here https://github.com/glamp/r-docker/blob/master/Dockerfile.
In short, use: RUN Rscript -e "install.packages('PACKAGENAME')". I have tried it and it works.
回答3:
You could write an R script with the desired install commands, then run it using Docker--if I'm reading this documentation correctly (https://hub.docker.com/_/r-base/).
FROM r-base
COPY . /usr/local/src/myscripts
WORKDIR /usr/local/src/myscripts
CMD ["Rscript", "myscript.R"]
Build your image with the command:
$ docker build -t myscript /path/to/Dockerfile
Where myscript.R contains the appropriate package installation commands.
回答4:
The R -e "install.packages..." approach does not always produce an error when package installation fails.
I wrote a script based on Cameron Kerr's answer here, which produces an error if the package cannot be loaded, and interrupts the Docker build process. It installs packages from either an R package repo, from GitHub, or from source given a full URL. It also prints the time taken to install, to help plan which packages to group together in one command.
Example usage in Dockerfile:
# Install from CRAN repo:
RUN Rscript install_packages_or_die.R https://cran.rstudio.com/ Cairo
RUN Rscript install_packages_or_die.R Cairo # Uses default CRAN repo
RUN Rscript install_packages_or_die.R jpeg png tiff # Multiple packages
# Install from GitHub:
RUN Rscript install_packages_or_die.R github ramnathv/htmlwidgets
RUN Rscript install_packages_or_die.R github timelyportfolio/htmlwidgets_spin spin
# Install from source given full URL of package:
RUN Rscript install_packages_or_die.R https://cran.r-project.org/src/contrib/Archive/curl/curl_4.0.tar.gz curl
Here's the script:
#!/usr/bin/env Rscript
# Install R packages or fail with error.
#
# Arguments:
# - First argument (optional) can be one of:
# 1. repo URL
# 2. "github" if installing from GitHub repo (requires that package 'devtools' is
# already installed)
# 3. full URL of package from which to install from source; if used, provide package
# name in second argument (e.g. 'curl')
# If this argument is omitted, the default repo https://cran.rstudio.com/ is used.
# - Remaining arguments are either:
# 1. one or more R package names, or
# 2. if installing from GitHub, the path containing username and repo name, e.g.
# 'timelyportfolio/htmlwidgets_spin', optionally followed by the package name (if
# it differs from the GitHub repo name, e.g. 'spin').
arg_list = commandArgs(trailingOnly=TRUE)
if (length(arg_list) < 1) {
print("ERROR: Too few arguments.")
quit(status=1, save='no')
}
if (arg_list[1] == 'github' || grepl("^https?://", arg_list[1], perl=TRUE)) {
if (length(arg_list) == 1) {
print("ERROR: No package name provided.")
quit(status=1, save='no')
}
repo = arg_list[1]
packages = arg_list[-1]
} else {
repo = 'https://cran.rstudio.com/'
packages = arg_list
}
for(i in seq_along(packages)){
p = packages[i]
start_time <- Sys.time()
if (grepl("^https?://[A-Za-z0-9.-]+/.+", repo, perl=TRUE)) {
# If 'repo' is URL with path after domain name, treat it as full path to a package
# to be installed from source.
install.packages(repo, repo=NULL, type="source");
} else if (repo == "github") {
# Install from GitHub.
github_path = p
elems = strsplit(github_path, '/')
if (lengths(elems) != 2) {
print("ERROR: Invalid GitHub path.")
quit(status=1, save='no')
}
username = elems[[1]][1]
github_repo_name = elems[[1]][2]
if (!is.na(packages[i+1])) {
# Optional additional argument was given specifying the R package name.
p = packages[i+1]
} else {
# Assume R package name is the same as GitHub repo name.
p = github_repo_name
}
library(devtools)
install_github(github_path)
} else {
# Install from R package repository.
install.packages(p, dependencies=TRUE, repos=repo);
}
end_time <- Sys.time()
if ( ! library(p, character.only=TRUE, logical.return=TRUE) ) {
quit(status=1, save='no')
} else {
cat(paste0("Time to install ", p, ":\n"))
print(end_time - start_time)
}
if (repo == "github") {
break
}
}
来源：https://stackoverflow.com/questions/45289764/install-r-packages-using-docker-file