Error Installing ggtree

[Vijay Ramesh]

Hi All,

I am new to using ggtree and have been trying to install the package by following the instructions mentioned on the github page. However, I am getting the error shown below. Any help would be much appreciated!

> source("https://bioconductor.org/biocLite.R")

Bioconductor version 3.4 (BiocInstaller 1.24.0), ?biocLite for help

> biocLite("ggtree")

BioC_mirror: https://bioconductor.org

Using Bioconductor 3.4 (BiocInstaller 1.24.0), R 3.3.0 (2016-05-03).

Installing package(s) ‘ggtree’

installation path not writeable, unable to update packages: cluster, codetools, foreign, lattice, Matrix,

  mgcv, nlme, survival

Old packages: 'party', 'spatstat'

Update all/some/none? [a/s/n]: 

a

I typed a to update all, but does not make a difference. 

Finally get this error:

Warning message:

package ‘ggtree’ is not available (for R version 3.3.0) 

-Vijay

[Vijay Ramesh]

Hi all,

Looks like the error was solved by updating to the latest version of R ("Sincere Pumpkin Patch"). 

However, this error of "Installation path not writeable" still persists.

installation path not writeable, unable to update packages: Matrix, mgcv, nlme, survival

[Yu, Guangchuang]

You need to have R >= 3.3.1 for ggtree, see https://github.com/Bioconductor-mirror/ggtree/blob/release-3.4/DESCRIPTION#L10.

​

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--

--~--~---------~--~----~------------~-------~--~----~

Guangchuang Yu, PhD Candidate
State Key Laboratory of Emerging Infectious Diseases
School of Public Health
The University of Hong Kong

Hong Kong SAR, China

www: https://guangchuangyu.github.io

-~----------~----~----~----~------~----~------~--~---

[Yu, Guangchuang]

On Tue, Feb 14, 2017 at 12:52 AM, Vijay Ramesh <vjj...@gmail.com> wrote:

Hi all,

Looks like the error was solved by updating to the latest version of R ("Sincere Pumpkin Patch"). 

However, this error of "Installation path not writeable" still persists.

installation path not writeable, unable to update packages: Matrix, mgcv, nlme, survival

You don’t have permission to write to the R installation path, so that you can’t update packages that come with R.

But you have permission to install R packages to a libPath that you have write permission.

You can check out library path by:

.libPaths()

On Monday, 13 February 2017 09:55:09 UTC-5, Vijay Ramesh wrote:

Hi All,

I am new to using ggtree and have been trying to install the package by following the instructions mentioned on the github page. However, I am getting the error shown below. Any help would be much appreciated!

> source("https://bioconductor.org/biocLite.R")

Bioconductor version 3.4 (BiocInstaller 1.24.0), ?biocLite for help

> biocLite("ggtree")

BioC_mirror: https://bioconductor.org

Using Bioconductor 3.4 (BiocInstaller 1.24.0), R 3.3.0 (2016-05-03).

Installing package(s) ‘ggtree’

installation path not writeable, unable to update packages: cluster, codetools, foreign, lattice, Matrix,

  mgcv, nlme, survival

Old packages: 'party', 'spatstat'

Update all/some/none? [a/s/n]: 

a

I typed a to update all, but does not make a difference. 

Finally get this error:

Warning message:

package ‘ggtree’ is not available (for R version 3.3.0) 

-Vijay

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​