docs: lint examples docs

luciorq · Dec 2, 2024 · bb0c823 · bb0c823
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diff --git a/R/create_env.R b/R/create_env.R
@@ -36,18 +36,20 @@
 #'
 #' @param overwrite Logical. Should environment always be overwritten?
 #'     Defaults to `FALSE`.
-#' @return An object of class `list` representing the result of the command execution.
-#'   Contains information about the standard output, standard error, and exit status of the command.
-#'   This function is used for its side effect of creating a Conda environment.
+#'
+#' @return An object of class `list` representing the result of the command
+#'   execution. Contains information about the standard output, standard error,
+#'   and exit status of the command.
+#'
 #' @examples
 #' \dontrun{
 #' # Create a Conda environment and install the CLI `fastqc` in it.
 #' condathis::create_env(
 #'   packages = "fastqc==0.12.1",
-#'   env_name = "fastqc_env",
+#'   env_name = "fastqc-env",
 #'   verbose = "output"
 #' )
-#' #> ! Environment fastqc_env succesfully created.
+#' #> ! Environment fastqc-env succesfully created.
 #' }
 #' @export
 create_env <- function(

diff --git a/R/env_exists.R b/R/env_exists.R
@@ -5,7 +5,7 @@
 #' and `FALSE` otherwise.
 #'
 #' @inheritParams create_env
-#' @return Boolean.
+#' @return Boolean. `TRUE` if the environment exists and `FALSE` otherwise.
 #' @examples
 #' \dontrun{
 #' # Create the environment

diff --git a/R/get_condathis_path.R b/R/get_condathis_path.R
@@ -1,6 +1,7 @@
 #' Retrieve System-Dependent Data Path for condathis
 #'
-#' Determines the appropriate user data directory for the `condathis` package based on the operating system. On macOS, it avoids using paths with spaces due to issues with `micromamba run` failing when there are spaces in the path.
+#' Determines the appropriate user data directory for the `condathis` package based on the operating system.
+#'   On macOS, it avoids using paths with spaces due to issues with `micromamba run` failing when there are spaces in the path.
 #'
 #' @details
 #' This function uses the `rappdirs` package to determine the user data directory.

diff --git a/R/install_packages.R b/R/install_packages.R
@@ -6,17 +6,20 @@
 #'
 #' @inheritParams create_env
 #'
-#' @return No value is returned; this function is used for its side effect of installing packages in a conda environment.
+#' @return An object of class `list` representing the result of the command
+#'   execution. Contains information about the standard output, standard error,
+#'   and exit status of the command.
+#'
 #' @examples
 #' \dontrun{
 #' condathis::create_env(
 #'   packages = "fastqc",
-#'   env_name = "fastqc_env"
+#'   env_name = "fastqc-env"
 #' )
-#' # Install the package `vim` in the `fastqc_env` environment.
+#' # Install the package `vim` in the `fastqc-env` environment.
 #' # It is not recommended to install multiple packages in the same environment,
 #  # as it defeats the purpose of isolation provided by separate environments.
-#' condathis::install_packages(packages = "vim", env_name = "fastqc_env")
+#' condathis::install_packages(packages = "vim", env_name = "fastqc-env")
 #' }
 #' @export
 install_packages <- function(packages,

diff --git a/R/list_packages.R b/R/list_packages.R
@@ -23,10 +23,10 @@
 #' # Creates a Conda environment with the CLI `fastqc`
 #' condathis::create_env(
 #'   packages = "fastqc",
-#'   env_name = "fastqc_env"
+#'   env_name = "fastqc-env"
 #' )
-#' # Lists the packages in env `fastqc_env`
-#' dat <- condathis::list_packages("fastqc_env")
+#' # Lists the packages in env `fastqc-env`
+#' dat <- condathis::list_packages("fastqc-env")
 #' dim(dat)
 #' #> [1] 34  8
 #' }

diff --git a/R/remove_env.R b/R/remove_env.R
@@ -4,8 +4,9 @@
 #'
 #' @inheritParams create_env
 #'
-#' @return An object of class `list` representing the result of the command execution.
-#'   Contains information about the standard output, standard error, and exit status of the command.
+#' @return An object of class `list` representing the result of the command
+#'   execution. Contains information about the standard output, standard error,
+#'   and exit status of the command.
 #'
 #' @examples
 #' \dontrun{

diff --git a/R/run_bin.R b/R/run_bin.R
@@ -1,20 +1,22 @@
-#' Run a Binary from a Conda Environment Without Emvironment Activation
+#' Run a Binary from a Conda Environment Without Environment Activation
 #'
 #' Executes a binary command from a specified Conda environment without activating the environment or using its environment variables. This function temporarily clears Conda and Mamba-related environment variables to prevent interference, ensuring that the command runs in a clean environment.
 #' Usually this is not what the user wants, check [run()] for the stable function to use.
 #'
 #' @inheritParams run
 #'
-#' @return An invisible list containing the results from `processx::run()`, including standard output and error.
+#' @return An object of class `list` representing the result of the command
+#'   execution. Contains information about the standard output, standard error,
+#'   and exit status of the command.
 #'
 #' @examples
 #' \dontrun{
-#' # Example assumes that 'my_env' exists and contains 'python'
-#' # Run 'python' with a script in 'my_env' environment
-#' condathis::run_bin("python", "script.py", env_name = "my_env", verbose = "silent")
+#' # Example assumes that 'my-env' exists and contains 'python'
+#' # Run 'python' with a script in 'my-env' environment
+#' condathis::run_bin("python", "script.py", env_name = "my-env", verbose = "silent")
 #'
 #' # Run 'ls' command with additional arguments
-#' condathis::run_bin("ls", "-la", env_name = "my_env")
+#' condathis::run_bin("ls", "-la", env_name = "my-env")
 #' }
 #'
 #' @export

diff --git a/README.md b/README.md
@@ -13,11 +13,13 @@ Run system command line interface (CLI) tools in a **reproducible** and
 
 ## Get started
 
-Install package from [CRAN](https://cran.r-project.org):
-
+<!--
+When available, install package from [CRAN](https://cran.r-project.org):
+&#10;
 ``` r
 install.packages("condathis")
 ```
+-->
 
 Install package from
 [R-Universe](https://luciorq.r-universe.dev/condathis):
@@ -30,6 +32,8 @@ install.packages("condathis", repos = c("https://luciorq.r-universe.dev", getOpt
 
 ``` r
 remotes::install_github("luciorq/condathis")
+# or
+pak::pkg_install("github::luciorq/condathis")
 ```
 
 ## Motivation
@@ -122,8 +126,8 @@ manages all the library dependencies of `fastqc`, making sure that they
 are compatible with the specific operating system.
 
 ``` r
-condathis::create_env(packages = "fastqc==0.12.1", env_name = "fastqc_env", verbose = "output")
-#> ! Environment fastqc_env succesfully created.
+condathis::create_env(packages = "fastqc==0.12.1", env_name = "fastqc-env", verbose = "output")
+#> ! Environment fastqc-env succesfully created.
 ```
 
 Then we run the command inside the environment just created which

diff --git a/man/create_base_env.Rd b/man/create_base_env.Rd
diff --git a/man/create_env.Rd b/man/create_env.Rd
diff --git a/man/define_platform.Rd b/man/define_platform.Rd
diff --git a/man/env_exists.Rd b/man/env_exists.Rd
diff --git a/man/format_channels_args.Rd b/man/format_channels_args.Rd
diff --git a/man/get_condathis_path.Rd b/man/get_condathis_path.Rd
diff --git a/man/install_packages.Rd b/man/install_packages.Rd
diff --git a/man/is_micromamba_available_for_arch.Rd b/man/is_micromamba_available_for_arch.Rd
diff --git a/man/list_packages.Rd b/man/list_packages.Rd
diff --git a/man/micromamba_user_installed.Rd b/man/micromamba_user_installed.Rd
diff --git a/man/native_cmd.Rd b/man/native_cmd.Rd