ggtree "open_tree" not found in linux version

Question

[Hongru]

I am trying to manipulate tree in R with ggtree package, but it says "Error: could not find function "open_tree"".

My system is: Ubuntu 14.04.4 LTS (GNU/Linux 4.2.0-27-generic x86_64)

The R version: R version 3.3.2 (2016-10-31) -- "Sincere Pumpkin Patch"

Answer 1

[Guangchuang Yu]

see https://guangchuangyu.github.io/ggtree/faq/#could-not-find-function.

[Hongru]

I am sorry I am a newbie to bioconductor. But I just installed ggtree yesterday (2017-01-09) with the biocLite("ggtree") command, so I assume it is the devel version you talked about in the post? If not, how can I install the devel version?

BTW, I did exactly the same thing with my mac, it worked perfectly, but not the linux.

[Guangchuang Yu]

you don't need to install devel version for using open_tree. You must install an outdated versioin.

see https://guangchuangyu.github.io/2016/07/how-to-bug-author/ and checkout your installation.

[Hongru]

Thanks for pointing to website, it helped! I found that I installed an outdated version of ggtree, and I further discovered that it is because my BiocInstaller version is outdated, so I followed this: http://bioconductor.org/install/#install-bioconductor-packages. Now problem solved, thanks again :-)