由于缺少GSL，GN程序包构建在Unix机器上失败 - GNU Scientific Library

Question

I am facing a particularly vexing problem with R package development. My own package, called ggstatsplot ( https://github.com/IndrajeetPatil/ggstatsplot ), depends on userfriendlyscience , which depends on another package called MBESS , which itself ultimately depends on another package called gsl . There is no problem at all for installation of ggstatsplot on a Windows machine (as assessed by AppVeyor continuous integration platform: https://ci.appveyor.com/project/IndrajeetPatil/ggstatsplot ).

But whenever the package is to be installed on Unix machines, it throws the error that ggstatsplot can't be downloaded because userfriendlyscience and MBESS can't be downloaded because gsl can't be downloaded. The same thing is also revealed on Travis continuous integration platform with virtual Unix machines, where the package build fails ( https://travis-ci.org/IndrajeetPatil/ggstatsplot ).

Now one way to solve this problem for the user on the Unix machine is to configure GSL (as described here: installing R gsl package on Mac ), but I can't possibly expect every user of ggstatsplot to go through the arduous process of configuring GSL . I want them to just run install.packages("ggstatsplot") and be done with it.

So I would really appreciate if anyone can offer me any helpful advice as to how I can make my package user's life simpler by removing this problem at its source. Is there something I should include in the package itself that will take care of this on behalf of the user?

Answer 1

This may not have a satisfying solution via changes to your R package (I'm not sure either way). If the gsl package authors (which include a former R Core member) didn't configure it to avoid a pre-req installation of a linux package, there's probably a good reason not to.

But it may be some consolation that most R+Linux users understand that some R packages first require installing the underlying Linux libraries ( eg , through apt or dnf / yum ).

Primary Issue: making it easy for the users to install

Try to be super clear on the GitHub readme and the CRAN INSTALL file . The gsl package has decent CRAN directions . This leads to the following bash code:

sudo apt-get install libgsl0-dev

The best example of clear (linux pre-req package) documentation I've seen is from the curl and sf packages. sf 's CRAN page lists only the human names of the 3 libraries, but the GitHub page provides the exact bash commands for three major distribution branches. The curl package does this very well too (eg, CRAN and GitHub ). For example, it provides the following explanation and bash code:

Installation from source on Linux requires libcurl . On Debian or Ubuntu use libcurl4-openssl-dev :

sudo apt-get install -y libcurl-dev

Ideally your documentation would describe how do install the gsl linux package on multiple distributions.

Disclaimer: I've never developed a package that directly requires a Linux package, but I use them a lot. In case more examples would help, this doc includes a script I use to install stuff on new Ubuntu machines. Some commands were stated explicitly in the package documentation; some had little or no documentation, and required research.

edit 2018-04-07 : I encountered my new favorite example: the sys package uses a config file to produce the following message in the R console. While installing 100+ packages on a new computer, it was nice to see this direct message, and not have to track down the R package and the documentation about its dependencies.

On Debian/Ubuntu this package requires AppArmor.

Please run: sudo apt-get install libapparmor-dev

Another good one is pdftools , that also uses a config file (and is also developed by Jeroen Ooms ).

Secondary Issue: installing on Travis

The userfriendly travis config file apparently installs a lot of binaries directly (including gsl ), unlike the current ggstatsplot version .

Alternatively, I'm more familiar with telling travis to install the linux package, as demonstrated by curl's config file . As a bonus, this probably more closely replicates what typical users do on their own machines.

addons:
  apt:
    packages:
    - libcurl4-openssl-dev

Follow up 2018-03-13 Indrajeet and I tweaked the travis file so it's working. Two sections were changed in the yaml file:

1. The libgsl0-dev entry was added under the packages section (similar to the libcurl4-openssl-dev entry above).
2. Packages were listed in the r_binary_packages section so they install as binaries. The build was timing out after 50 minutes, and now it's under 10 min. In this particular package, the r_binary_packages section was nested in the Linux part of the Travis matrix so it wouldn't interfere with his two OS X jobs on Travis.