---
title: Troubleshooting
output: rmarkdown::html_document
vignette: |
    %\VignetteIndexEntry{troubleshooting}
    %\usepackage[utf8]{inputenc}
    %\VignetteEngine{knitr::rmarkdown}
---

**Updated:** ***`r format(Sys.Date(), '%b-%d-%Y')`***  

This vignette provides troubleshooting tips for common issues encountered when
using the `MotifPeeker` package.  

If you encounter an issue that is not covered, please open an issue on the
[GitHub repository](https://github.com/neurogenomics/MotifPeeker/issues).  

<br>

#### MEME Suite Related

1. **Error: Cannot find MEME Suite**  
    If You have ensured that the MEME Suite is installed, but still encounter
    this error, set the path to the MEME suite binaries (`.../meme/bin/`) using
    the `meme_path` parameter in the `MotifPeeker()` function call.  

2. **Error: Failed to generate .html file.**  
    Please ensure that the
    [Perl dependencies required by the MEME Suite](https://meme-suite.org/meme/doc/install.html#prereq_perl)
    are installed, particularly `XML::Parser`, which can be installed using the
    following command in the terminal:  
    ```bash
    cpan install XML::Parser
    ```

#### `MotifPeeker()` Related

1. **Function takes too long to run**  
    It is likely motif discovery is what is taking too long to run. Try
    reducing the number of workers if you are running out of memory while
    running the `MotifPeeker()` function.  
    Additionally, follow the [runtime guidance](https://neurogenomics.github.io/MotifPeeker/articles/MotifPeeker.html#runtime)
    for `MotifPeeker()`.  


# Session Info 

<details> 

```{r session-info}
utils::sessionInfo()
```

</details>  

<br>
