MISC: for several problems

1. remove renv.lock since it only work for Apple Silicon because the hash sum
2. ignore the R files in pre-commit since renv::restore() will modify it.
3. Update the documentation for R package installation.

.gitignore

@@ -30,3 +30,6 @@ __pycache__/
 # Rust files
 /Cargo.lock
 /target/
+
+# renv
+/renv.lock

.pre-commit-config.yaml

@@ -5,6 +5,7 @@ repos:
     rev: v4.5.0
     hooks:
     -   id: trailing-whitespace
+        exclude: .*\.R
     -   id: end-of-file-fixer
     -   id: check-toml
     -   id: check-yaml

docs/installation.md

@@ -5,6 +5,7 @@
 1. [rustup](https://rustup.rs/)
 2. (Optional) [samtools](http://www.htslib.org/) and
    [bedops](https://bedops.readthedocs.io/en/latest/) for executing `smc2bed-all`
+3. (Optional) R for plotting
 
 ```bash
 # Install rustup
@@ -15,12 +16,51 @@ brew install samtools bedops
 wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
 bash Miniconda3-latest-Linux-x86_64.sh
 conda install -c bioconda samtools bedops
+# Install R
+sudo apt-get install r-base
+# Or
+brew install r
+# Restore the environment
+R -e "renv::restore()"
+R -e "renv::install('./R/argweaver')"
 # And then, install
 pip install argweavers+git://github.com/tcztzy/argweaver
 # OR from pypi
 pip install argweavers
 ```
 
+## Notions for R package
+
+### `ape`
+If you are using macOS with Apple Silicon, you may also face the following error while install `ape`:
+
+```
+fatal error: pcre.h: No such file or directory
+```
+
+You can fix it by installing `pcre` using homebrew:
+
+```bash
+brew install pcre
+```
+
+And then export `CFLAGS`:
+```bash
+export CFLAGS="-I/opt/homebrew/include"
+```
+
+### `RPHAST`
+
+Since the RPHAST package is not available on CRAN, you need to install it from
+GitHub. Since the original RPHAST package is not compatible with the latest
+version of R, you need to install the coregenomics/RPHAST@bugfix/f77_call branch from GitHub. [See here for the details](https://github.com/CshlSiepelLab/RPHAST/pull/6).
+
+```R
+devtools::install_github("coregenomics/RPHAST@bugfix/f77_call")
+```
+
+
+
 ## Build from source
 
 ```console