Our group publishes R packages (for internal use) to a CRAN-like repository. Users have complained (rightly) that the documentation isn't very accessible to them without firing up R and doing ?function_name interactively.
So I would like to build a website with the documentation for all the versions of the R packages my group has created.
If I do pkgdown::build_site() in my package's top-level directory, that creates a nice self-contained tree docs/ containing HTML files with all the docs for that package. It even has a prominent version number at the top of every page, which is nice.
Now I'd like to situate that document tree in a larger site, so that a user can browse to the package they're looking for, look at previous versions, etc. Is that something someone's set up a solution for?
I'm thinking that the docs/ directory could simply be rsync'd to a web server, building the path from info in DESCRIPTION, e.g.:
Rscript -e 'pkgdown::build_site()'
mkdir -p r-docs/MyPackage # Replace with real package name
mv docs r-docs/MyPackage/1.3.1 # Replace with real version
rsync -avz r-docs/ example.com:r-docs/
But this gets a bit awkward to do repeatedly - is there some support for this use case in pkgdown or another similar package (not necessarily tied to pkgdown, would use whatever's most appropriate)?
Related
My package is hosted in github, and user can install it through devtools::install_github.
Now I'm using pkgdown to generate documentation site, which created a 10M docs folder. Then I found devtools::install_github always download the whole master zip ball which become quite slow.
I tried to exclude the docs folder with these attempts:
.Rbuildignore, turned out it's only about bundled package, while install_github is installing source package so it doesn't work.
put package in pkg folder, put the generated docs folder out of pkg folder. However the whole master zip ball is always downloaded, even with subdir = "pkg" specified.
put development in a branch, and to create a special package branch without docs folder. Merge two branch but let package branch exclude docs folder. I tried make .gitignore to be branch specific but it doesn't seem to work. This seemed to be impossible.
My newest attempt is to create a separate repo solely for the website, just let pkgdown create the website in that folder like build_site(path = "../docsite/docs"). This should solve the problem and is simple and clean. The only imperfection is the website url will not be the usually pattern.
EDIT: with the latest version of pkgdown, there is no path parameter anymore, you need to specify it in the site configuration yaml, which works better (you don't need to specify it in every command).
I use a cluster (OS is Linux) which does not have R. I would like to install R in my personal folders so that I can just do
Rscript example.R arg1 arg2
How should I install R on this cluster knowing that I don't have admin rights?
How can I then manage the packages?
I'm not sure this is on-topic, but: all you really have to do is
download the R source tarball from CRAN; unpack it somewhere in your file space
create an r-build directory at the same level of the hierarchy (not technically necessary, but it's better practice to keep the source and build directories separate)
create an installation directory (say ~/r_install) somewhere sensible within your file space
cd to the source directory; tools/rsync-recommended
cd to the build directory
../[srcdir]/configure --prefix=~/r_install
make (to build the binaries)
make install (to move everything where it belongs; not technically necessary, as you can run R from the build directory)
Where this may get hairy is with all of the system requirements for R (LaTeX, Java, bzip2, etc. etc. ...) it is theoretically possible to download all this stuff and install it in your own file space, but it starts to get sufficiently tedious that it will be easier to beg your sysadmin to install at least the dependencies for you ...
as #Hack-R points out the basics of this answer are already present on Unix & Linux stackexchange, although my answer is a little more detailed ...
I've found several posts about best practice, reproducibility and workflow in R, for example:
How to increase longer term reproducibility of research (particularly using R and Sweave)
Complete substantive examples of reproducible research using R
One of the major preoccupations is ensuring portability of code, in the sense that moving it to a new machine (possibly running a different OS) is relatively straightforward and gives the same results.
Coming from a Python background, I'm used to the concept of a virtual environment. When coupled with a simple list of required packages, this goes some way to ensuring that the installed packages and libraries are available on any machine without too much fuss. Sure, it's no guarantee - different OSes have their own foibles and peculiarities - but it gets you 95% of the way there.
Does such a thing exist within R? Even if it's not as sophisticated. For example simply maintaining a plain text list of required packages and a script that will install any that are missing?
I'm about to start using R in earnest for the first time, probably in conjunction with Sweave, and would ideally like to start in the best way possible! Thanks for your thoughts.
I'm going to use the comment posted by #cboettig in order to resolve this question.
Packrat
Packrat is a dependency management system for R. Gives you three important advantages (all of them focused in your portability needs)
Isolated : Installing a new or updated package for one project won’t break your other projects, and vice versa. That’s because packrat gives each project its own private package library.
Portable: Easily transport your projects from one computer to another, even across different platforms. Packrat makes it easy to install the packages your project depends on.
Reproducible: Packrat records the exact package versions you depend on, and ensures those exact versions are the ones that get installed wherever you go.
What's next?
Walkthrough guide: http://rstudio.github.io/packrat/walkthrough.html
Most common commands: http://rstudio.github.io/packrat/commands.html
Using Packrat with RStudio: http://rstudio.github.io/packrat/rstudio.html
Limitations and caveats: http://rstudio.github.io/packrat/limitations.html
Update: Packrat has been soft-deprecated and is now superseded by renv, so you might want to check this package instead.
The Anaconda package manager conda supports creating R environments.
conda create -n r-environment r-essentials r-base
conda activate r-environment
I have had a great experience using conda to maintain different Python installations, both user specific and several versions for the same user. I have tested R with conda and the jupyter-notebook and it works great. At least for my needs, which includes RNA-sequencing analyses using the DEseq2 and related packages, as well as data.table and dplyr. There are many bioconductor packages available in conda via bioconda and according to the comments on this SO question, it seems like install.packages() might work as well.
It looks like there is another option from RStudio devs, renv. It's available on CRAN and supersedes Packrat.
In short, you use renv::init() to initialize your project library, and use renv::snapshot() / renv::restore() to save and load the state of your library.
I prefer this option to conda r-enviroments because here everything is stored in the file renv.lock, which can be committed to a Git repo and distributed to the team.
To add to this:
Note:
1. Have Anaconda installed already
2. Assumed your working directory is "C:"
To create desired environment -> "r_environment_name"
C:\>conda create -n "r_environment_name" r-essentials r-base
To see available environments
C:\>conda info --envs
.
..
...
To activate environment
C:\>conda activate "r_environment_name"
(r_environment_name) C:\>
Launch Jupyter Notebook and let the party begins
(r_environment_name) C:\> jupyter notebook
For a similar "requirements.txt", perhaps this link will help -> Is there something like requirements.txt for R?
Check out roveR, the R container management solution. For details, see https://www.slideshare.net/DavidKunFF/ownr-technical-introduction, in particular slide 12.
To install roveR, execute the following command in R:
install.packages("rover", repos = c("https://lair.functionalfinances.com/repos/shared", "https://lair.functionalfinances.com/repos/cran"))
To make full use of the power of roveR (including installing specific versions of packages for reproducibility), you will need access to a laiR - for CRAN, you can use our laiR instance at https://lair.ownr.io, for uploading your own packages and sharing them with your organization you will need a laiR license. You can contact us on the email address in the presentation linked above.
Question: How do I move all of the most up-to-date R packages into one simple location that R (and everything else) will use from now and forever for my packages?
I have been playing around with R on Ubuntu 10.04 using variously RGedit, RCmdr, R shell, and RStudio. Meanwhile, I have installed packages, updated packages, and re-updated packages via apt, synaptic, install.packages(), etc... which apparently means these packages get placed everywhere, and (with the occasional sudo tossed in) with different permissions.
Currently I have different versions of different (and repeated) packages in:
/home/me/R/i486-pc-linux-gnu-library/2.10
/home/me/R/i486-pc-linux-gnu-library/2.14
/home/me/R/i486-pc-linux-gnu-library/
/usr/local/lib/R/site-library
/usr/lib/R/site-library
/usr/lib/R/library
First - I'm a single user, on a single machine - I don't want multiple library locations, I just want it to work.
Second - I am on an extremely slow connection, and can't keep just downloading packages repeatedly.
So - is there an easy way to merge all these library locations into one simple location? Can I just copy the folders over?
How do I set it in concrete that this is and always will be where anything R related looks for and updates packages?
This is maddening.
Thanks for your help.
Yes, it should almost work to just copy the folders over. But pre-2.14 packages WITHOUT a NAMESPACE file probably won't work in R 2.14 where all packages must have a namespace...
And you'd want to manually ensure you only copy the latest version of each package if you have multiple versions...
If you type .libPaths(), it will tell you where R looks for packages. The first in the list is where new packages are typically installed. I suspect that .libPaths() might return different things from RStudio vs. Rcmd etc.
After piecing together various bits of info here goes: A complete moron's guide to the R packages directory organization:
NB1 - this is my experience with Ubuntu - your mileage may vary
NB2 - I'm a single user on a single machine, and I like things simple.
Ubuntu puts anything installed via apt, or synaptic in:
/usr/lib/R/site-library
/usr/lib/R/library
directories. The default vanilla R install will try install packages here:
/usr/local/lib/R/site-library
Since these are system directories the user does not have write privileges to, depending on what method you are interacting with R you might be prompted with a friendly - "Hey buddy - we can't write there, you want us to put your packages in your home directory?" which seems innocent and reasonable enough... assuming you never change your GUI, or your working environment. If you do, the new GUI / environment might not be looking in the directory where the packages were placed, so won't find them. (Most interfaces have a way for you to point where your personal library of packages is, but who wants to muck about in config files?)
What seems to be the best practice for me (and feel free to correct me if I'm wrong) with a default install setup on Ubuntu, is to do any package management from a basic R shell as sudo: > sudo R and from there do your install.packages() voodoo. This seems to put packages in the usr/local/lib/R/site-library directory.
At the same time, update.packages() will update the files in /usr/lib/R/site-library and usr/lib/R/library directories, as well as usr/local/lib/R/site-library
(As for usr/lib/R/ division, it looks like /library/ has the core packages, while /site-library/ holds anything added, assuming they were installed by apt...)
Any packages previously installed and in the wrong place can be moved to the /usr/local/lib/R/site-library directory (assuming you are sudoing it) just by moving the directories (thanks #Tommy), but as usr/lib/R/ is controlled by apt - best not add or subtract anything from there...
Whew. Anyway - simple enough, and in simple language. Thanks everyone for the help.
Does R have a dependency management tool to facilitate project-specific dependencies? I'm looking for something akin to Java's maven, Ruby's bundler, Python's virtualenv, Node's npm, etc.
I'm aware of the "Depends" clause in the DESCRIPTION file, as well as the R_LIBS facility, but these don't seem to work in concert to provide a solution to some very common workflows.
I'd essentially like to be able to check out a project and run a single command to build and test the project. The command should install any required packages into a project-specific library without affecting the global R installation. E.g.:
my_project/.Rlibs/*
Unfortunately, Depends: within the DESCRIPTION: file is all you get for the following reasons:
R itself is reasonably cross-platform, but that means we need this to work across platforms and OSs
Encoding Depends: beyond R packages requires encoding the Depends in a portable manner across operating systems---good luck encoding even something simple such as 'a PNG graphics library' in a way that can be resolved unambiguously across systems
Windows does not have a package manager
AFAIK OS X does not have a package manager that mixes what Apple ships and what other Open Source projects provide
Even among Linux distributions, you do not get consistency: just take RStudio as an example which comes in two packages (which all provide their dependencies!) for RedHat/Fedora and Debian/Ubuntu
This is a hard problem.
The packrat package is precisely meant to achieve the following:
install any required packages into a project-specific library without affecting the global R installation
It allows installing different versions of the same packages in different project-local package libraries.
I am adding this answer even though this question is 5 years old, because this solution apparently didn't exist yet at the time the question was asked (as far as I can tell, packrat first appeared on CRAN in 2014).
Update (November 2019)
The new R package renv replaced packrat.
As a stop-gap, I've written a new rbundler package. It installs project dependencies into a project-specific subdirectory (e.g. <PROJECT>/.Rbundle), allowing the user to avoid using global libraries.
rbundler on Github
rbundler on CRAN
We've been using rbundler at Opower for a few months now and have seen a huge improvement in developer workflow, testability, and maintainability of internal packages. Combined with our internal package repository, we have been able to stabilize development of a dozen or so packages for use in production applications.
A common workflow:
Check out a project from github
cd into the project directory
Fire up R
From the R console:
library(rbundler)
bundle('.')
All dependencies will be installed into ./.Rbundle, and an .Renviron file will be created with the following contents:
R_LIBS_USER='.Rbundle'
Any R operations run from within this project directory will adhere to the project-speciic library and package dependencies. Note that, while this method uses the package DESCRIPTION to define dependencies, it needn't have an actual package structure. Thus, rbundler becomes a general tool for managing an R project, whether it be a simple script or a full-blown package.
You could use the following workflow:
1) create a script file, which contains everything you want to setup and store it in your projectd directory as e.g. projectInit.R
2) source this script from your .Rprofile (or any other file executed by R at startup) with a try statement
try(source("./projectInit.R"), silent=TRUE)
This will guarantee that even when no projectInit.R is found, R starts without error message
3) if you start R in your project directory, the projectInit.R file will be sourced if present in the directory and you are ready to go
This is from a Linux perspective, but should work in the same way under windows and Mac as well.