rapids/README.md

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# RAPIDS

**R**eproducible **A**nalysis **Pi**peline for **D**ata **S**treams

For more information refer to our [documentation](http://www.rapids.science)

By [MoSHI](https://www.moshi.pitt.edu/), [University of Pittsburgh](https://www.pitt.edu/)

## Installation 

For RAPIDS installation refer to to the [documentation](https://www.rapids.science/1.8/setup/installation/)

### For the installation of the Docker version

1. Follow the [instructions](https://www.rapids.science/1.8/setup/installation/) to setup RAPIDS via Docker (from scratch).

2. Delete current contents in /rapids/ folder when in a container session.
    ```
    cd ..
    rm -rf rapids/{*,.*}
    cd rapids
    ```

3. Clone RAPIDS workspace from Git and checkout a specific branch.
    ```
    git clone "https://repo.ijs.si/junoslukan/rapids.git" .
    git checkout <branch_name>
    ```

4. Install missing “libpq-dev” dependency with bash.
    ```
    apt-get update -y
    apt-get install -y libpq-dev
    ```

5. Restore R venv.
Type R to go to the interactive R session and then:
    ```
    renv::restore()
    ```

6. Install cr-features module 
From: https://repo.ijs.si/matjazbostic/calculatingfeatures.git -> branch modifications_for_rapids. 
Then follow the "cr-features module" section below.  

7. Install all required packages from environment.yml, prune also deletes conda packages not present in environment file.
    ```
    conda env update --file environment.yml –prune
    ```

8. If you wish to update your R or Python venvs.
    ```
    R in interactive session:
    renv::snapshot()
    Python: 
    conda env export --no-builds | sed 's/^.*libgfortran.*$/  - libgfortran/' | sed 's/^.*mkl=.*$/  - mkl/' >  environment.yml
    ```

### cr-features module 

This RAPIDS extension uses cr-features library accessible [here](https://repo.ijs.si/matjazbostic/calculatingfeatures).

To use cr-features library:

- Follow the installation instructions in the [README.md](https://repo.ijs.si/matjazbostic/calculatingfeatures/-/blob/master/README.md).

- Copy built calculatingfeatures folder into the RAPIDS workspace.

- Install the cr-features package by:
    ```
    pip install path/to/the/calculatingfeatures/folder
    e.g. pip install ./calculatingfeatures if the folder is copied to main parent directory
    cr-features package has to be built and installed everytime to get the newest version. 
    Or an the newest version of the docker image must be used.   
    ```

## Updating RAPIDS

To update RAPIDS, first pull and merge [origin]( https://github.com/carissalow/rapids), such as with:

```commandline
git fetch --progress "origin" refs/heads/master
git merge --no-ff origin/master
```

Next, update the conda and R virtual environment.

```bash
R -e 'renv::restore(repos = c(CRAN = "https://packagemanager.rstudio.com/all/__linux__/focal/latest"))'
```

## Custom configuration
### Credentials

As mentioned under [Database in RAPIDS documentation](https://www.rapids.science/1.6/snippets/database/), a `credentials.yaml` file is needed to connect to a database.
It should contain:

```yaml
PSQL_STRAW:
  database: staw
  host: 212.235.208.113
  password: password
  port: 5432
  user: staw_db
```

where`password` needs to be specified as well.

## Possible installation issues
### Missing dependencies for RPostgres

To install `RPostgres` R package (used to connect to the PostgreSQL database), an error might occur:

```text
------------------------- ANTICONF ERROR ---------------------------
Configuration failed because libpq was not found. Try installing:
   * deb: libpq-dev (Debian, Ubuntu, etc)
   * rpm: postgresql-devel (Fedora, EPEL)
   * rpm: postgreql8-devel, psstgresql92-devel, postgresql93-devel, or postgresql94-devel (Amazon Linux)
   * csw: postgresql_dev (Solaris)
   * brew: libpq (OSX)
If libpq is already installed, check that either:
  (i)  'pkg-config' is in your PATH AND PKG_CONFIG_PATH contains a libpq.pc file; or
  (ii) 'pg_config' is in your PATH.
If neither can detect , you can set INCLUDE_DIR
and LIB_DIR manually via:
  R CMD INSTALL --configure-vars='INCLUDE_DIR=... LIB_DIR=...'
--------------------------[ ERROR MESSAGE ]----------------------------
  <stdin>:1:10: fatal error: libpq-fe.h: No such file or directory
compilation terminated.
```

The library requires `libpq` for compiling from source, so install accordingly.

### Timezone environment variable for tidyverse (relevant for WSL2)

One of the R packages, `tidyverse` might need access to the `TZ` environment variable during the installation.
On Ubuntu 20.04 on WSL2 this triggers the following error:

```text
> install.packages('tidyverse')

ERROR: configuration failed for package ‘xml2’
System has not been booted with systemd as init system (PID 1). Can't operate.
Failed to create bus connection: Host is down
Warning in system("timedatectl", intern = TRUE) :
  running command 'timedatectl' had status 1
Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) :
  namespace ‘xml2’ 1.3.1 is already loaded, but >= 1.3.2 is required
Calls: <Anonymous> ... namespaceImportFrom -> asNamespace -> loadNamespace
Execution halted
ERROR: lazy loading failed for package ‘tidyverse’
```

This happens because WSL2 does not use the `timedatectl` service, which provides this variable.

```bash
~$ timedatectl
System has not been booted with systemd as init system (PID 1). Can't operate.
Failed to create bus connection: Host is down
```

and later 

```bash 
Warning message:
In system("timedatectl", intern = TRUE) :
  running command 'timedatectl' had status 1
Execution halted
```

This can be amended by setting the environment variable manually before attempting to install `tidyverse`:

```bash
export TZ='Europe/Ljubljana'
```

## Possible runtime issues
### Unix end of line characters

Upon running rapids, an error might occur:

```bash
/usr/bin/env: ‘python3\r’: No such file or directory
```

This is due to Windows style end of line characters. 
To amend this, I added a `.gitattributes` files to force `git` to checkout `rapids` using Unix EOL characters.
If this still fails, `dos2unix` can be used to change them.

### System has not been booted with systemd as init system (PID 1)

See [the installation issue above](#Timezone-environment-variable-for-tidyverse-(relevant-for-WSL2)).