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News: new package ggtree in devel branch
4
3.7 years ago by
Guangchuang Yu1.0k
China/Guangzhou/Southern Medical University
Guangchuang Yu1.0k wrote:

This package is designed for viewing and annotating phylogenetic tree.

Please check out the vignettes: http://www.bioconductor.org/packages/3.1/bioc/vignettes/ggtree/inst/doc/ggtree.html

modified 3.7 years ago by remi.tournebize10 • written 3.7 years ago by Guangchuang Yu1.0k
0
3.7 years ago by
United States
Dawid G. Nowak10 wrote:

Hi,

I was trying to install you package: 'ggtree' and getting all the time the warning that package 'ggtree' is not available (for R version 3.1.2). Any clue what is going on?

Thanks,

Dawid

-------

source("http://bioconductor.org/biocLite.R")
biocLite("ggtree")

BioC_mirror: http://bioconductor.org
Using Bioconductor version 3.0 (BiocInstaller 1.16.1), R version 3.1.2.
Installing package(s) 'ggtree'
Warning message:
package 'ggtree' is not available (for R version 3.1.2)

2

You can't install a devel package using the current release version of R. You have to use R-devel.

http://bioconductor.org/developers/how-to/useDevel/

1

Now you can use biocLite("ggtree") in R version 3.2.0 to install the ggtree package.

You can also use the following command to install it:

install.packages("ggtree",
repos = "http://www.bioconductor.org/packages/devel/bioc",
type  = "source")


If it throw error for Bioconductor dependencies, use biocLite to install those dependent pkgs.

2

Please do not install packages 'by hand', this will lead to corrupt installations that are then very tedious to debug. Use biocLite(). If you must have a devel package 'now', then use the appropriate version of R and Bioconductor as indicated by the link provided by Jim MacDonald.

totally agree.

0
3.7 years ago by
France
remi.tournebize10 wrote:

Hello,

This is a neat package! Is it possible by any mean to plot onto tree branches points at given times (not simply at the nodes)?

Thank you for this great job, hope the package will be stable released soon,

Rémi