ggtree installation

Guangchuang Yu edited this page Sep 21, 2016 · 9 revisions

Install ggtree is easy, follow the guide in the page, http://bioconductor.org/packages/ggtree/:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
# biocLite("BiocUpgrade") # you may need this
biocLite("ggtree")

In Linux or Mac (if your R was install via brew), you may have problems when compiling some of the dependent packages (e.g. EBImage).

If you have problems, you can contact me. I will be glad if I can help.

When the problem was solved, I will update this page to record how it was solved.

If you solved your installation problem, please help editing this page. It will help new users.

If you want to share your experience, please provide the following information:

  • Operating System
  • Package manager
  • Package/library name
  • R package

Different Linux distributions use different package manager (e.g. yum and apt) and package name may different slightly, so these information are needed for users to install dependent library (e.g. libtiff) for R package (e.g. EBImage).

EBImage

EBImage is used to read pictures (e.g. Phylopic or user's own pictures) and it depends on a number of third-party packages, including tiff and fftwtools.

On RedHat, you need to install:

sudo yum install libtiff-devel fftw-devel

On Ubuntu 16.04.1 LTS, you need to install:

sudo apt-get install libfftw3-3 libfftw3-dev libtiff5-dev
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