CSOgroup · Arvindiyer · Jun 5, 2026 · Jun 5, 2026 · Jun 5, 2026
diff --git a/.Rbuildignore b/.Rbuildignore
@@ -5,8 +5,4 @@
 ^pkgdown$
 ^\.github$
 ^INSTALLATION\.md$
-^environment\.yml$
-^CONTRIBUTING\.md$
-^CODE_OF_CONDUCT\.md$
 ^dev$
-^cran-comments\.md$
diff --git a/CODE_OF_CONDUCT.md → .github/CODE_OF_CONDUCT.md b/CODE_OF_CONDUCT.md → .github/CODE_OF_CONDUCT.md
diff --git a/CONTRIBUTING.md → .github/CONTRIBUTING.md b/CONTRIBUTING.md → .github/CONTRIBUTING.md
diff --git a/.gitignore b/.gitignore
@@ -7,6 +7,9 @@
 .ipynb_checkpoints
 inst/doc
 docs/
+*.tar.gz
+src/*.so
+src/*.o
 .*
 !/.gitignore
 !/.github
diff --git a/INSTALLATION.md b/INSTALLATION.md
@@ -1,48 +1,133 @@
-## Installation
+# Installation
 
-- You can install the development version of SelectSim from
-  [GitHub](https://github.com/CSOgroup/SelectSim) with:
+## Prerequisites
 
-``` r
+SelectSim requires **R ≥ 3.5** and includes compiled C++ code via `Rcpp` and `RcppArmadillo`.
+Before installing, make sure you have a working C++ compiler:
+
+- **macOS** — Install Xcode Command Line Tools: `xcode-select --install`
+- **Linux** — Install build tools, e.g. on Ubuntu/Debian: `sudo apt install build-essential`
+- **Windows** — Install [Rtools](https://cran.r-project.org/bin/windows/Rtools/) and ensure it is on your PATH
+
+---
+
+## Option 1 — Install from GitHub (standard)
+
+Install directly from GitHub using `pak`:
+
+```r
+# install.packages("pak")
+pak::pak("CSOgroup/SelectSim")
+```
+
+Or using `devtools` (legacy):
+
+```r
 # install.packages("devtools")
-devtools::install_github("CSOgroup/SelectSim",dependencies = TRUE, build_vignettes = TRUE)
+devtools::install_github("CSOgroup/SelectSim", dependencies = TRUE, build_vignettes = TRUE)
 ```
 
-## Installation with micromamba enviorment (prefered)
+---
 
+## Option 2 — Install with micromamba (recommended)
 
-`micromamba` is a tiny version of the mamba package manager (Like Conda). Refer [website](https://mamba.readthedocs.io/en/latest/installation/micromamba-installation.html) for it's installation guide.
+[micromamba](https://mamba.readthedocs.io/en/latest/installation/micromamba-installation.html) provides a fully isolated, reproducible R environment. This is the **recommended approach** if you are on a shared server, HPC cluster, or want to avoid conflicts with your existing R installation.
 
-Steps to follow after installing micromamba in a terminal:
+### Step 1 — Install micromamba
 
-`micromamba create -n r_env`\
-`micromamba activate r_env`\
-`micromamba install conda-forge::r-base`\
-`micromamba install conda-forge::r-essentials`\
-`micromamba install conda-forge::r-devtools`\
-`micromamba install conda-forge::r-pak`\
-`micromamba install conda-forge::cmake`\
-`micromamba install conda-forge::r-rcppparallel`\
-`micromamba install conda-forge::r-rfast`
+Follow the [official micromamba installation guide](https://mamba.readthedocs.io/en/latest/installation/micromamba-installation.html) for your platform.
 
-- After this run R and install `SelectSim` R package as follows
-``` r
-# install.packages("devtools")
-devtools::install_github("CSOgroup/SelectSim",dependencies = TRUE, build_vignettes = TRUE)
+### Step 2 — Create and activate an R environment
+
+```bash
+micromamba create -n r_env
+micromamba activate r_env
 ```
-OR
-``` r
-library('pak')
-pak::pkg_install('CSOgroup/SelectSim')
+
+### Step 3 — Install R and required system dependencies
+
+```bash
+micromamba install \
+  conda-forge::r-base \
+  conda-forge::r-essentials \
+  conda-forge::r-devtools \
+  conda-forge::r-pak \
+  conda-forge::cmake \
+  conda-forge::r-rcppparallel \
+  conda-forge::r-rfast
 ```
 
-Alternative way install with provided [`enviorment.yml`](enviorment.yml) file.
+### Step 4 — Install SelectSim inside R
 
-`micromamba create -f enviorment.yml`\
-`micromamba activate r_env`
-- After this run R and install `SelectSim` R package as follows
-``` r
-# install.packages("devtools")
-devtools::install_github("CSOgroup/SelectSim",dependencies = TRUE, build_vignettes = TRUE)
+```r
+# install.packages("pak")
+pak::pak("CSOgroup/SelectSim")
+```
+
+---
+
+## Option 3 — Restore the exact development environment
+
+A fully pinned conda environment file is provided at [`dev/environment.yml`](dev/environment.yml).
+This reproduces the exact software stack (R version, all system libraries) used during development.
+
+```bash
+micromamba create -f dev/environment.yml
+micromamba activate r_env
 ```
 
+Then install SelectSim:
+
+```r
+pak::pak("CSOgroup/SelectSim")
+```
+
+> **Note:** The environment file pins exact package versions and is Linux-specific (linux-64).
+> It may not work on macOS or Windows.
+
+---
+
+## Verifying the installation
+
+After installing, confirm everything works with a quick test run:
+
+```r
+library(SelectSim)
+data(luad_run_data, package = "SelectSim")
+
+result <- selectX(
+  M                = luad_run_data$M,
+  sample.class     = luad_run_data$sample.class,
+  alteration.class = luad_run_data$alteration.class,
+  n.cores          = 1,
+  min.freq         = 10,
+  n.permut         = 10    # small number for a quick smoke test
+)
+```
+
+A successful run returns a list with a `result` data frame of evolutionary dependencies.
+For a full analysis, use `n.permut = 1000` or higher.
+
+---
+
+## Troubleshooting
+
+**`rfast` fails to install**
+`rfast` requires a Fortran compiler.
+On macOS, install `gfortran` from [mac.r-project.org/tools](https://mac.r-project.org/tools/).
+On Linux, install via your package manager (e.g. `sudo apt install gfortran`).
+With micromamba, `conda-forge::r-rfast` handles this automatically.
+
+**Vignettes not building**
+Ensure `pandoc` is installed (`pandoc --version` in a terminal).
+Install via `brew install pandoc` (macOS), `sudo apt install pandoc` (Linux), or through the micromamba environment (`conda-forge::pandoc`).
+
+**Compilation errors on Windows**
+Ensure Rtools is installed and its `bin/` directory is on your PATH.
+Run `pkgbuild::check_build_tools()` in R to verify your toolchain is detected correctly.
+
+**Vignettes missing after install**
+`pak::pak()` does not build vignettes by default. If you need the vignettes locally, use:
+```r
+devtools::install_github("CSOgroup/SelectSim", dependencies = TRUE, build_vignettes = TRUE)
+```
diff --git a/README.Rmd b/README.Rmd
@@ -35,8 +35,8 @@ This package accompanies the manuscript:
 You can install the development version of SelectSim from [GitHub](https://github.com/CSOgroup/SelectSim) with:
 
 ``` r
-# install.packages("devtools")
-devtools::install_github("CSOgroup/SelectSim", dependencies = TRUE, build_vignettes = TRUE)
+# install.packages("pak")
+pak::pak("CSOgroup/SelectSim")
 ```
 
 For more details on installation refer to [INSTALLATION](INSTALLATION.md).

diff --git a/README.md b/README.md
@@ -38,8 +38,8 @@ You can install the development version of SelectSim from
 [GitHub](https://github.com/CSOgroup/SelectSim) with:
 
 ``` r
-# install.packages("devtools")
-devtools::install_github("CSOgroup/SelectSim", dependencies = TRUE, build_vignettes = TRUE)
+# install.packages("pak")
+pak::pak("CSOgroup/SelectSim")
 ```
 
 For more details on installation refer to

diff --git a/cran-comments.md → dev/cran-comments.md b/cran-comments.md → dev/cran-comments.md
diff --git a/environment.yml → dev/environment.yml b/environment.yml → dev/environment.yml
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