# System requirements

The set up for the rawrr package needs to be run in order to use the rawDiag package. 

Therfore, please follow the install notes of the rawrr package.

1. Go to https://bioconductor.org/packages/release/bioc/install/rawrr/INSTALL
to find installation notes for the rawrr package.

2. Follow the instructions provided on the webpage.

3. After installing rawrr, open your R shell.

4. Type and run the following commands:

```
rawrr::installRawFileReaderDLLs()
rawrr::installRawrrExe()
```

These commands install necessary components. Make sure to execute them in your R shell.

By following these steps, you'll successfully set up rawrr,
enabling you to use the rawDiag package seamlessly.


The `Dockerfile` performing `R CMD build` and `R CMD check` requires

```
from bioconductor/bioconductor_docker:devel
run apt-get update && apt-get install mono-mcs mono-xbuild -y
run apt-get install texlive-base texlive-latex-extra texinfo texlive-fonts-extra -y
## rawrr
run R -q -e "BiocManager::install(c('BiocStyle', 'ExperimentHub', 'knitr', 'protViz', 'rmarkdown', 'tartare', 'testthat'))"
## rawDiag
run R -q -e "BiocManager::install(c('rawrr', 'gglplot2', 'hexbin', 'BiocParallel', 'reshape2', 'scales'))"
```


# Installation from scratch

```
install.packages('BiocManager')

## install rawDiag imports

pkg <- c('dplyr', 'ggplot2', 'grDevices', 'hexbin', 'htmltools', 'BiocStyle',
  'BiocParallel', 'rawrr', 'rlang', 'reshape2', 'scales', 'shiny', 'stats',
  'utils')

pkg[!(pkg %in% installed.packages())] |> BiocManager::install()
```

## add packages for checking

```
pkg  <- c('roxygen2', 'ExperimentHub', 'testthat', 'knitr', 'rmarkdown', 'tartare')
pkg[!(pkg %in% installed.packages())] |> BiocManager::install()
```