> For the complete documentation index, see [llms.txt](https://docs.finngen.fi/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://docs.finngen.fi/working-in-the-sandbox/quirks-and-features/r-and-python-local-repositories-in-finngen-sandbox.md).

# Install R and Python packages from the local Sandbox repository

Users can install R and Python packages from the local Sandbox repository.

{% hint style="info" %}
Users can request new packages to be added to the local Sandbox repository ([please see policy](https://finngen.gitbook.io/finngen-handbook/working-in-the-sandbox/quirks-and-features/sandbox-ivm-tool-request-handling-policy)).
{% endhint %}

## R packages

### List R packages available in the local Sandbox CRAN repository using R

The Sandbox IVM has been pre-configured to use the local Sandbox CRAN repository. The `available.packages()` R command can be used to list the available packages in the local Sandbox CRAN repository.

Use the following command to list all available packages and their versions:

```
available.packages()[,c("Package","Version")]
```

You can search available packages by name. For example, use the following command to list all packages that start with 'Bi':

```
p <- available.packages()[,c("Package", "Version")] 
c <- grepl("^Bi", p[,c("Package")], ignore.case=TRUE) 
p[c,]
```

The `available.packages()`command returns other columns as well. You can list them all using the `colnames` command:

```
colnames(available.packages())
```

### List R packages available in the local Sandbox CRAN repository using the terminal

You can list packages using the `R` command line program with the `-e` option following other instructions in the previous section.

List all packages:

```
R -e 'available.packages()[,c("Package","Version")]'
```

Search packages by name:

```
R -e 'p <- available.packages()[,c("Package", "Version")];c <- grepl("^Bi", p[,c("Package")], ignore.case=TRUE);p[c,]'
```

You can also directly list the packages in the local Sandbox CRAN repository:

```
ls /usr/finngen-repos/cran/source/src/contrib
```

### Install R packages from the local Sandbox CRAN repository

The Sandbox IVM has been pre-configured to use the local Sandbox CRAN repository. Use the `install.packages("package name")` R command to install packages from the local Sandbox CRAN repository.

For example, the following command installs the Biobase package:

```
install.packages("Biobase")
```

{% hint style="info" %}
Packages are installed in your Sandbox IVM persistent disk. The exact location depends on the R version, for example, /home/ivm/Rx86\_64-pc-linux-gnu-library/4.3. Installed packages are automatically detected by R only from this location. When using a different version of R, you may need to use the .libPaths() variable to define the location of the package (more information is available [here).](https://www.rdocumentation.org/packages/base/versions/3.6.2/topics/libPaths) You can also install the same package for different R versions.
{% endhint %}

### List available R packages in the local Sandbox CRAN repository outside the Sandbox

It is possible to list the available R packages outside Sandbox by using buckets.

R packages are available in the following bucket:

```
gs://fg-production-master_cran/source/src/contrib
```

You can see the contents of the bucket using the cloud console:

<https://console.cloud.google.com/storage/browser/fg-production-master_cran/source/src/contrib;tab=objects?project=fg-production-master>

or the `gsutil` command line program:

```
gsutil ls gs://fg-production-master_cran/source/src/contrib
```

## Python packages

### List Python packages available in the local Sandbox PyPI repository using the terminal

The Sandbox IVM has been pre-configured to use the Sandbox PyPI repository on GCP Artifact Registry: <https://europe-west1-python.pkg.dev/finngen-sandbox-v3-containers/pypi/simple/>. It contains packages for Python 3. FinnGen uses the `pip` program to install Python packages in the Sandbox.

Use the following command to list available Python 3 packages:

```
python3 -m pip list --index-url https://europe-west1-python.pkg.dev/finngen-sandbox-v3-containers/pypi/simple/
```

### Install Python packages from the local Sandbox PyPI repository using the terminal

Use the following command to install a Python 3 package:

```
python3 -m pip install <packagename>
```

{% hint style="info" %}
**Notice for Debian 12 Users:** To comply with PEP 668 and prevent system instability, global package installation via `pip` is blocked by default. The recommended and safest fix is to isolate your packages using a [virtual environment](https://finngen.gitbook.io/finngen-handbook/working-in-the-sandbox/quirks-and-features/python-virtual-environment-in-sandbox) before executing your `pip install` commands. Alternatively, if you explicitly require a global installation and accept the risk of breaking system-managed utilities, you can bypass this restriction for a single command by appending the `--break-system-packages` flag.
{% endhint %}

{% hint style="info" %}
Python lmod modules with preinstalled scientific python packages are available in the sandbox. You can read about them [here](/working-in-the-sandbox/which-tools-are-available/anaconda-python-module-with-ready-set-of-scientific-packages.md).
{% endhint %}