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News: new package `ggtree` in devel branch
4
gravatar for Guangchuang Yu
2.8 years ago by
Hong Kong
Guangchuang Yu800 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

 

any comments are welcome.

ADD COMMENTlink modified 2.8 years ago by remi.tournebize10 • written 2.8 years ago by Guangchuang Yu800
0
gravatar for Dawid G. Nowak
2.8 years ago by
United States
Dawid G. Nowak0 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) 
 

ADD COMMENTlink written 2.8 years ago by Dawid G. Nowak0
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/

ADD REPLYlink written 2.8 years ago by James W. MacDonald45k
1

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

ADD REPLYlink written 2.6 years ago by Guangchuang Yu800

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.

 

ADD REPLYlink written 2.7 years ago by Guangchuang Yu800
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.

ADD REPLYlink written 2.7 years ago by Martin Morgan ♦♦ 20k

totally agree.

ADD REPLYlink written 2.7 years ago by Guangchuang Yu800
0
gravatar for remi.tournebize
2.8 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

ADD COMMENTlink written 2.8 years ago by remi.tournebize10

Can you explain more clear? I don't get your idea.

ADD REPLYlink written 2.7 years ago by Guangchuang Yu800
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