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remotes, a small step of devtools suite, a big step for my Travis carrer

Posted on One min read

Beginning

Back to my graduate year, I set up Travis to automatically test my R packages.

Development

devtools is a good tools, but there are a few issues:

  1. install_bioc() only works well in development version
  2. even that, install_bioc() would promote you to type y to install BiocInstaller. But it’s hard to response to that, since Travis CI is automatic. So I have to manually install BiocInstaller before calling it.
  3. Due to a misunderstanding 1, only in development version can install_github() & install_local() install dependencies on GitHub

Climax

The newly release version of remotes works very nice. (devtools is splited, install_*() is moved to remotes and exported back)

It just needs Git on your system (no BiocInstaller at all), and it’s very lightweight, only needs severval seconds to install.

Afterword

By the way, the new BiocManager is also very nice. You can install it as a normal CRAN package, no more source("https://bioconductor.org/biocLite.R") (The damn network speed never troubles me any more, 何以解忧，唯有镜像.)

  1. It’s a misconception started before the first I use R on Travis, the exact point should be the first time that I write Remotes in DESCRIPTION. At that time, I think I just need to specify GitHub packages in Remotes. But devtools doesn’t install these packages, I even switch to Github version of devtools.

    Thanks to this SO answer, I know that I have to both specify package location in Imports and add package name in Depends. Acutally, all I need to avoid the caveat is to read the official documentation:

    You can mark any regular dependency defined in the Depends, Imports, Suggests or Enhances fields as being installed from a remote location by adding the remote location to Remotes in your DESCRIPTION file.

    注：原文来自 2018-06-03 的 post：It’s me rather than devtools who is wrong | 错的并不是devtools，而是我 ↩︎