Install a local R package with dependencies from C

问题:

I have built an R package, i.e. I have the mypackage.tar.gz file. This package depends on several other packages, all downloadable and installable from any CRAN mirror.

Now I want to install this package on a system where the dependencies are not yet installed, and I would like that the dependencies will be downloaded and installed automatically when I install my package.

I tried:

install.packages("mypackage.tar.gz",type="source",dependencies=TRUE,repos="http://a.cran.mirror")

but it searches for mypackage.tar.gz on the mirror (and obviously it does not find), while if I set repos=NULL it correctly tries to install the local package file (as documented), but obviously it does not find the dependencies packages.

So my question is: is there a way to perform a 'mixed' installation (local package with online dependencies) or the only way to do is to manually install all the dependencies?

回答1:

You could use install from the devtools package. Just run install("<directory of your package>", dependencies = TRUE). Its help states:

Uses R CMD INSTALL to install the package. Will also try to install dependencies of the package from CRAN, if they're not already installed.

回答2:

If you already have installed your local package, you should be able to use a couple functions in tools to install the dependencies from CRAN:

library('tools')
installFoundDepends(pkgDepends('mypackage', local = FALSE)$Found)

Note: You can pass args (like repos) through installFoundDepends to install.packages.

You can also use the Depends element from the pkgDepends output to pass directly to install.packages:

install.packages(pkgDepends('mypackage')$Depends)

UPDATE: Apparently it is not possible to install a local package with dependencies=FALSE. This seems odd, since you can do that for a remote package from a repository. The reason (looking at the source code) is that if(is.null(repos) & missing(contriburl)), installation is handled via system calls to R CMD INSTALL, which has no dependency-related arguments.

回答3:

Here, I'm using untar() with devtools::install() and passing in a directory to which the source tarball has been extracted.

d <- tempdir()
untar("mypackage.tar.gz", compressed="gzip", exdir=d)
devtools::install(file.path(d, "mypackage"), dependencies=TRUE,
                  repos="https://cloud.r-project.org/")

If you want to install from multiple repos, you can provide a list of them. For example, to use both Bioconductor and CRAN, you could run:

 devtools::install(file.path(d, "mypackage"), dependencies=TRUE,
                   repos=BiocInstaller::biocinstallRepos())

NOTE: I can't figure out how to directly pass the tarball to install(), but this solution works in the meantime and leaves no clutter because we extract to a temp directory. It seems install_local() should be able to take a tarball, but I am getting an error when attempting to do so.

回答4:

I personally use RStudio which tells you which dependencies are missing. Then I copy the string in the arguments of the following small script to change the 'strange' symbols in classical " (xclip is copying to clipboard [it is like pbcopy on macOS]).

#!/bin/bash
echo $@ | sed 's/‘/"/g' | sed 's/’/"/g' | xclip -selection clipboard

Then I simply use install.packages(c(ctrl_v__what_to_install)) and R starts to install all the dependencies.

NB: remember that the two ‘ written in the above script are different and the first time you copy this script, I advise to copy again the original quotation marks characters.