I need to include several bash scripts in the R package I'm writing. I'd love to distribute them together with the package, so when a user installs the package via devtools::install_github(...) he/she gets the scripts as well.
I know it is possible, but I don't know how. Including the files in the scripts subdirectory doesn't seem to suffice. I need a means to tell R (or RStudio) to include them.
I use RStudio for development, so I would appreciate a solution that integrates with the "Build package" functionality that RStudio provides.
Simply add whatever you want to the inst/xxx folder in your package.
The folder will get installed as xxx when you compile/publish the package as a library.
You access the files via system.file(), e.g.
system.file('scripts/peak_mem.sh', package='clustertools')
See more details on the R packages by Hadley Wickham
Thank you #Axeman!
Related
I have created a package in R. It is all fully documented and written according to R package guidelines. I have used devtools to generate documentation.
document("/home/rstudio/EndoMineR/")
However when I try to use ?EndoMineR I get the error:
No documentation for ‘EndoMineR’ in specified packages and libraries:
you could try ‘??EndoMineR’
How can I create the help files for my package? What am I likely to be missing?
As additional information, when I click the package name in R studio I get the help files but not if I try ?EndoMineR. Also the .Rd files in the man directory (which I think is what devtools::document() generates) seem to be updating just fine. I assume the ?EndoMiner accesses the man files so I'm not sure why this folder is not accessible (it is top level)
I made an R package for personal use, but the way I load it is by individual files. Such as:
source("../compr/R/compr.R")
source("../compr/R/error_df.R")
source("../compr/R/rmse.R")
I would like to load the entire package, which is called compr, as I would other libraries.
If you are using RStudio, I would suggest creating a project and setting it to your compr directory. After that you will be able to use devtools::load_all() to load your package directly.
If you don't want to do this, or you don't use RStudio devtools::load_all('path/to/compr') will also work.
P.S. compr directory needs to be the root of the package i.e. the place where your DESCRIPTION file is.
I have been doing research and I can't quite figure out how to build my R package, that calls C functions, in order for it to work in both Windows and Linux environments. I am building the package on a Linux machine.
I have two C files, one.C and two.C, I place the two files in the src directory after using package.skeleton(...). In the namespace file I use the command: useDynLib(one,two). Is this correct? Or do I need to put the actual function names instead of the file names? Do I need to export the function names?
Do I need to put the .so files in the src directory or will these be created automatically? I am worried then it won't work on a windows machine which needs a .dll file.
As you can see I'm a little confused, thanks for the help.
One of the standard R manuals is Writing R Extensions. Part of this manual is the section 5 System and foreign language interfaces. This will probably answer the majority of your questions. In regard to the dynamically linked libraries (dll or so), they are built on the fly. You develop your package, including the C code. Once you want to install the library from source (e.g. using R CMD INSTALL spam), or create a binary distribution, the C code will be compiled into the appropriate library file.
Faced with similar headaches I switched to C++ in combination with Rcpp. Rcpp takes care of all the headaches for you in compiling packages:
http://dirk.eddelbuettel.com/code/rcpp.html
There is also an entire vignette on how to build a package using Rcpp:
http://dirk.eddelbuettel.com/code/rcpp/Rcpp-package.pdf
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.