R notebook error: installation path not writeable

October 07, 2019 19:29
4 comments

When using your default R notebook configuration, I am getting an error that I cannot update dependency packages using BiocManager because the installation path is not writeable.

I am also unable to open the Bioconductor preconfigured notebook. When i select it, it asks for a few minutes to create a new runtime, but always keeps the default R configuration.

Comments

4 comments

Sushma Chaluvadi
- October 08, 2019 13:44
Hi Beth,

The team is investigating and we will get bak to you with an update!

0
Beri
- October 08, 2019 15:42
Hi Beth,

What do you mean by "Bioconductor preconfigured notebooks"?

0
Elizabeth Sheets
- Edited October 08, 2019 16:15
The second option under the runtime configuration environment:

0
Beri
- October 09, 2019 20:07
Hi Beth,

I spoke with the dev team and they mentioned most of these are already installed and current
```
pkgs = c("Rsamtools", "data.table", "qqman", "RColorBrewer", "tidyr", "dplyr")
pkgs %in% rownames(installed.packages())
```
A better strategy would be to install only packages that are not yet installed
```
pkgs = pkgs[!pkgs %in% rownames(installed.packages())]
```
which may only be qqman.

For Bioconductor, where Rsamtools comes from, the recommend installation approach for CRAN or Bioconductor packages is
```
BiocManager::install(pkgs)
```
or to install new packages and update any out-of-date packages with
```
BiocManager::install(pkgs, ask=FALSE)
```
0

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