The R Manuals

https://rstudio.github.io/r-manuals
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### R Configuration Summary Example

Source: https://rstudio.github.io/r-manuals/r-admin/Platform-notes.html

This is an example of the expected output from the 'configure' script, indicating detected interfaces, external libraries, and additional capabilities. Ensure these match your system's installed packages.

```text
Interfaces supported:      X11, tcltk
External libraries:        pcre2, readline, curl
Additional capabilities:   PNG, JPEG, TIFF, NLS, cairo, ICU
```

--------------------------------

### Start HTML Help System

Source: https://rstudio.github.io/r-manuals/r-intro/Packages.html

Initiates the HTML-based help system, allowing you to browse documentation for installed packages. Navigate to the 'Reference' section to find package listings.

```R
> help.start()
```

--------------------------------

### Install and Check Source Package

Source: https://rstudio.github.io/r-manuals/r-admin/Add-on-packages.html

Install a source package and then check it. The output of the installation is redirected to a log file.

```bash
R CMD INSTALL -l libdir pkg > pkg.log 2>&1
R CMD check -l libdir --install=check:pkg.log pkg
```

--------------------------------

### Run Examples for an R Help Topic

Source: https://rstudio.github.io/r-manuals/r-intro/Introduction-and-preliminaries.html

Execute the example code provided within the help documentation for a specific topic using the `example()` function. Replace `topic` with the actual name of the help topic.

```r
> example(topic)
```

--------------------------------

### Getting Help on R Functions

Source: https://rstudio.github.io/r-manuals/r-exts/Creating-R-packages.html

Use the `?` operator to access help pages for R functions like `library()` and `INSTALL`.

```R
?library
?INSTALL
```

--------------------------------

### Configure and Build R

Source: https://rstudio.github.io/r-manuals/r-admin/Installing-R-under-Unix-alikes.html

Standard commands to configure, build, and check the R installation before installing.

```bash
./configure
make
make check
```

--------------------------------

### Install R Manuals (Info and PDF)

Source: https://rstudio.github.io/r-manuals/r-admin/Installing-R-under-Unix-alikes.html

Installs the info and PDF versions of the R manuals. 'prefix', 'libdir', or 'rhome' can be optionally specified.

```bash
make install-info
```

```bash
make install-pdf
```

--------------------------------

### Create R Installation Directory

Source: https://rstudio.github.io/r-manuals/r-admin/Platform-notes.html

Create the base directory for R installations and set ownership. This is a prerequisite for installing R components.

```bash
sudo mkdir -p /opt/R/arm64
sudo chown -R $USER /opt/R
```

--------------------------------

### Install and log R package

Source: https://rstudio.github.io/r-manuals/r-exts/Creating-R-packages.html

Install an R package to a specified library directory and capture the installation log. This is a prerequisite for checking an installed package.

```bash
R CMD INSTALL -l libdir pkg > pkg.log 2>&1
```

--------------------------------

### License Specification Examples

Source: https://rstudio.github.io/r-manuals/r-exts/Creating-R-packages.html

Examples of how to specify package licenses in the DESCRIPTION file, including single licenses, multiple alternatives, and custom terms.

```text
License: GPL-2
License: LGPL (>= 2.0, < 3) | Mozilla Public License
License: GPL-2 | file LICENCE
License: GPL (>= 2) | BSD_3_clause + file LICENSE
License: Artistic-2.0 | AGPL-3 + file LICENSE
```

--------------------------------

### Install R

Source: https://rstudio.github.io/r-manuals/r-admin/Installing-R-under-Unix-alikes.html

Command to install the R tree to the system after configuration and building.

```bash
make install
```

--------------------------------

### Install Package from Local Zip on Windows

Source: https://rstudio.github.io/r-manuals/r-admin/Add-on-packages.html

On Windows, `install.packages` can install a binary package from a local zip file by setting `repos` to `NULL`.

```R
install.packages("path/to/package.zip", repos = NULL)
```

--------------------------------

### Install R Packages with Dependencies (R Session)

Source: https://rstudio.github.io/r-manuals/r-admin/Add-on-packages.html

Install a package and all its dependencies that are not already installed. Use dependencies = TRUE to ensure all required packages are fetched.

```r
> install.packages("Rcmdr", dependencies = TRUE)
```

--------------------------------

### Navigate to and Start R Session (Subsequent)

Source: https://rstudio.github.io/r-manuals/r-intro/Introduction-and-preliminaries.html

For subsequent R sessions, first navigate to your existing working directory and then start the R program.

```bash
$ cd work
$ R
```

--------------------------------

### Efficiently Installing Symbols with Rf_install

Source: https://rstudio.github.io/r-manuals/r-exts/System-and-foreign-language-interfaces.html

Shows a pattern for frequently installing symbols by caching the SEXP result. This avoids repeated lookups in the symbol table.

```c
static SEXP VerSymbol = NULL;
...
if (VerSymbol == NULL) VerSymbol = Rf_install("version");
```

--------------------------------

### Install R Run-time Tests

Source: https://rstudio.github.io/r-manuals/r-admin/Installing-R-under-Unix-alikes.html

Installs the run-time tests for R, populating a 'tests' directory within the installation.

```bash
make install-tests
```

--------------------------------

### Run R Installation Tests

Source: https://rstudio.github.io/r-manuals/r-admin/Installing-R-under-Unix-alikes.html

Navigate to the R installation's home directory and execute these commands to run various test suites for your R installation. Use `check-devel` for development-related tests and `check-all` for comprehensive testing.

```bash
cd tests
../bin/R CMD make check
../bin/R CMD make check-devel
../bin/R CMD make check-all
```

--------------------------------

### R CMD INSTALL with Configure Arguments

Source: https://rstudio.github.io/r-manuals/r-exts/Creating-R-packages.html

This command demonstrates how to install the RODBC package, providing custom configuration arguments to the configure script for specifying ODBC include and library paths, and the ODBC manager.

```bash
R CMD INSTALL \
  --configure-args='--with-odbc-include=/opt/local/include \
  --with-odbc-lib=/opt/local/lib --with-odbc-manager=iodbc' \
  RODBC
```

--------------------------------

### Package Overview Alias Example

Source: https://rstudio.github.io/r-manuals/r-exts/Writing-R-documentation-files.html

An example of an \alias entry for a package overview page. This convention allows access to the package overview using package?pkgname.

```Rd
utils-package
```

--------------------------------

### Install R to a Custom Directory

Source: https://rstudio.github.io/r-manuals/r-admin/Installing-R-under-Unix-alikes.html

Installs R to a specified directory using the 'prefix' variable with 'make install'. This method is primarily for GNU make.

```bash
make prefix=/path/to/here install
```

--------------------------------

### Installing Java Development Kit on Debian/Ubuntu

Source: https://rstudio.github.io/r-manuals/r-admin/Essential-and-useful-other-programs-under-a-Unix-alike.html

Command to install the default Java Development Kit (JDK) on Debian or Ubuntu systems.

```bash
sudo apt install default-jdk
```

--------------------------------

### Install Source Package on Windows

Source: https://rstudio.github.io/r-manuals/r-admin/Add-on-packages.html

Use `install.packages(type="source")` to install source packages on Windows. Additional tools are needed for packages with compiled code.

```R
install.packages(type="source")
```

--------------------------------

### Start R Program from Command Line

Source: https://rstudio.github.io/r-manuals/r-intro/Invoking-R.html

Use the 'R' command to start the main R program. Options can control session behavior, and input/output can be redirected.

```bash
R [options] [<infile] [>outfile]
```

--------------------------------

### Install Package for Specific Sub-architecture

Source: https://rstudio.github.io/r-manuals/r-admin/Add-on-packages.html

On multi-architecture installations, use R CMD INSTALL --libs-only pkg to install only the compiled libraries for a specific sub-architecture. This is typically used on Windows or Unix-alikes with specific build configurations.

```bash
R CMD INSTALL --libs-only pkg
```

--------------------------------

### List Installed Java Versions

Source: https://rstudio.github.io/r-manuals/r-admin/Platform-notes.html

Check for compatible Java versions installed on your system, specifying the architecture.

```bash
/usr/libexec/java_home -V -a arm64
```

```bash
/usr/libexec/java_home -V -a x86_64
```

--------------------------------

### Install R Framework to Custom Location

Source: https://rstudio.github.io/r-manuals/r-admin/Platform-notes.html

Specify a custom installation directory for the R framework during the build process.

```bash
make prefix=/where/you/want/R.framework/to/go install
```

--------------------------------

### Install Stripped Executables and Libraries

Source: https://rstudio.github.io/r-manuals/r-admin/Installing-R-under-Unix-alikes.html

Installs stripped executables and libraries to reduce file size, supported on platforms where stripping is available.

```bash
make install-strip
```

--------------------------------

### Install Subversion for Intel Macs

Source: https://rstudio.github.io/r-manuals/r-admin/Platform-notes.html

Download and install the subversion client for Intel (x86_64) architecture. This involves downloading a tarball, extracting it, and copying the executable to a system path.

```bash
curl -OL https://mac.r-project.org/tools/subversion-1.14.3-darwin15.6.tar.gz
tar xf subversion-1.14.3-darwin15.6.tar.gz
sudo cp subversion-1.14.3-darwin15.6/svn $LOCAL/bin
```

--------------------------------

### RODBC Example: Channel Finalization

Source: https://rstudio.github.io/r-manuals/r-exts/System-and-foreign-language-interfaces.html

An example demonstrating the use of R_MakeExternalPtr and R_RegisterCFinalizerEx in the RODBC package to manage database connections.

```APIDOC
## RODBC Channel Finalization Example

### Description
This example shows how the RODBC package uses external pointers to manage database connections. A C finalizer is registered to close the connection when the external pointer is no longer needed.

### Code Snippet
```c
    SEXP ans, ptr;
    ans = PROTECT(Rf_allocVector(INTSXP, 1));
    ptr = R_MakeExternalPtr(thisHandle, Rf_install("RODBC_channel"), R_NilValue);
    PROTECT(ptr);
    R_RegisterCFinalizerEx(ptr, chanFinalizer, TRUE);
            ...
    /* return the channel no */
    INTEGER(ans)[0] = nChannels;
    /* and the connection string as an attribute */
    Rf_setAttrib(ans, Rf_install("connection.string"), constr);
    Rf_setAttrib(ans, Rf_install("handle_ptr"), ptr);
    UNPROTECT(3);
    return ans;
```

### Finalizer Function Example
```c
static void chanFinalizer(SEXP ptr)
{
    if(!R_ExternalPtrAddr(ptr)) return;
    inRODBCClose(R_ExternalPtrAddr(ptr));
    R_ClearExternalPtr(ptr); /* not really needed */
}
```
```

--------------------------------

### Run R Examples with Valgrind

Source: https://rstudio.github.io/r-manuals/r-exts/Debugging.html

Execute R scripts or R CMD check examples under Valgrind for memory debugging. Use specific Valgrind tools and options for detailed analysis.

```bash
R -d valgrind --vanilla < mypkg-Ex.R
```

```bash
R -d "valgrind --tool=memcheck --leak-check=full" --vanilla < mypkg-Ex.R
```

```bash
--use-valgrind
```

--------------------------------

### Install Subversion for Apple Silicon

Source: https://rstudio.github.io/r-manuals/r-admin/Platform-notes.html

Download and install the subversion client for Apple Silicon (arm64) architecture. This involves downloading a tarball, extracting it, and copying the executable to a system path.

```bash
curl -OL https://mac.r-project.org/tools/subversion-1.14.3-darwin.20-arm64.tar.gz
tar xf subversion-1.14.3-darwin.20-arm64.tar.gz 
sudo cp subversion-1.14.3-darwin-20-arm64/svn $LOCAL/bin
```

--------------------------------

### Install R as a Shared/Static Library

Source: https://rstudio.github.io/r-manuals/r-admin/Installing-R-under-Unix-alikes.html

Installs R as a shared or static library into the system's library directory. 'prefix' is optional, and 'libdir' offers more precise control.

```bash
make prefix=/path/to/here install-libR
```

--------------------------------

### Get linker flags using pkg-config for shared R library

Source: https://rstudio.github.io/r-manuals/r-exts/Linking-GUIs-and-other-front-ends-to-R.html

If R is installed and pkg-config is available, use it to get linker flags for a shared R library. This assumes no sub-architectures or macOS frameworks are used.

```bash
pkg-config --libs libR
```

--------------------------------

### Get C++ flags using pkg-config for shared R library

Source: https://rstudio.github.io/r-manuals/r-exts/Linking-GUIs-and-other-front-ends-to-R.html

If R is installed and pkg-config is available, use it to get C++ flags for a shared R library. This assumes no sub-architectures or macOS frameworks are used.

```bash
pkg-config --cflags libR
```

--------------------------------

### Rf_installChar

Source: https://rstudio.github.io/r-manuals/r-exts/API-index.html

Installs a character string as a symbol.

```APIDOC
## Rf_installChar

### Description
Installs a character string as a symbol.

### Attributes
This function is related to attributes in R.

### Finding and setting variables
This function is also related to finding and setting variables.
```

--------------------------------

### Device Creation and Initialization Example

Source: https://rstudio.github.io/r-manuals/r-ints/Graphics-Devices.html

Illustrates the process of creating and initializing a new graphics device using R's graphics engine functions. This includes checking API version, allocating device descriptions, and adding the device to the engine.

```c
    pGEDevDesc gdd;

    R_GE_checkVersionOrDie(R_GE_version);
    R_CheckDeviceAvailable();
    BEGIN_SUSPEND_INTERRUPTS {
        pDevDesc dev;
        /* Allocate and initialize the device driver data */
        if (!(dev = GEcreateDD()))
            return 0; /* or error() */
        /* set up device driver or free 'dev' and error() */
        gdd = GEcreateDevDesc(dev);
        GEaddDevice2(gdd, "dev_name");
    } END_SUSPEND_INTERRUPTS;
```

--------------------------------

### Get Tcl Auto Path

Source: https://rstudio.github.io/r-manuals/r-exts/Creating-R-packages.html

Retrieves the Tcl auto_path, which is used to find Tcl libraries. This is useful when installing Tcl extensions like BWidget.

```R
library(tcltk)
strsplit(tclvalue('auto_path'), " ")[[1]]
```

--------------------------------

### Display 'configure' Help

Source: https://rstudio.github.io/r-manuals/r-admin/Configuration-on-a-Unix-alike.html

Run this command to see a list of all available configuration options for R.

```bash
./configure --help
```

--------------------------------

### Install R Dependencies via curl and tar

Source: https://rstudio.github.io/r-manuals/r-admin/Platform-notes.html

Manually download and install binary components like pcre2 and xz for R development. Ensure you use the correct component version (e.g., darwin23 for Sonoma on Apple Silicon).

```bash
curl -OL https://mac.r-project.org/bin/darwin23/arm64/pcre2-10.44-darwin.23-arm64.tar.xz
sudo tar -xvzf pcre2-10.44-darwin.23-arm64.tar.gz -C /
curl -OL https://mac.r-project.org/bin/darwin23/arm64/xz-5.6.3-darwin.23-arm64.tar.xz
sudo tar -xvzf xz-5.6.3-darwin.23-arm64.tar.xz -C /
```

--------------------------------

### Check and List Outdated R Packages

Source: https://rstudio.github.io/r-manuals/r-admin/Add-on-packages.html

Use `packageStatus()` to get information on installed and available packages. Filter the results to show packages that are not 'ok'.

```R
> inst <- packageStatus()$inst
> inst[inst$Status != "ok", c("Package", "Version", "Status")]
                  Package Version      Status
Biobase           Biobase   2.8.0 unavailable
RCurl               RCurl   1.4-2     upgrade
Rgraphviz       Rgraphviz  1.26.0 unavailable
rgdal               rgdal  0.6-27     upgrade
```

--------------------------------

### Install R with Custom R Home Directory

Source: https://rstudio.github.io/r-manuals/r-admin/Installing-R-under-Unix-alikes.html

Installs R using a version-specific R home directory, useful for managing multiple R versions on non-Debian 64-bit Linux systems.

```bash
make install rhome=/usr/local/lib64/R-4.7.0 Under development
```

--------------------------------

### Get Default Packages in R

Source: https://rstudio.github.io/r-manuals/r-admin/Add-on-packages.html

Displays the default set of packages loaded when R starts. This can be customized by setting the 'defaultPackages' option in startup code.

```r
> getOption("defaultPackages")
[1] "datasets"  "utils"     "grDevices" "graphics"  "stats"     "methods"
```

--------------------------------

### Install R Packages from Source (Command Line)

Source: https://rstudio.github.io/r-manuals/r-admin/Add-on-packages.html

Use this command in a terminal to install R packages from source. Specify the library path with -l, or omit it to use the default R session library.

```bash
R CMD INSTALL -l /path/to/library pkg1 pkg2 ...
```

--------------------------------

### Vignette Metadata: Index Entry

Source: https://rstudio.github.io/r-manuals/r-exts/Creating-R-packages.html

Example of a LaTeX comment used to specify vignette metadata, specifically the index entry for a vignette. This is processed at package installation time.

```tex
%\VignetteIndexEntry{Using Animal}
```

--------------------------------

### Creating and Linking Subdirectory Libraries

Source: https://rstudio.github.io/r-manuals/r-exts/Creating-R-packages.html

Demonstrates how to create and link to a library built from code in a subdirectory. Ensure all necessary dependencies are explicitly managed.

```makefile
.PHONY: all mylibs

all: $(SHLIB)
$(SHLIB): mylibs

mylibs:
        (cd subdir; $(MAKE))
```

--------------------------------

### Get Help for a Specific Function in R

Source: https://rstudio.github.io/r-manuals/r-intro/Introduction-and-preliminaries.html

Use `help()` to access documentation for a specific R function. This is useful for understanding function arguments, return values, and examples.

```r
> help(solve)
```

--------------------------------

### Initialize Custom Input/Output Streams

Source: https://rstudio.github.io/r-manuals/r-exts/The-R-API.html

Set up R's internal serialization streams for custom input and output media using R_InitInPStream and R_InitOutPStream.

```c
void R_InitInPStream(R_inpstream_t stream, R_pstream_data_t data,
                     R_pstream_format_t type,
                     int (*inchar)(R_inpstream_t),
                     void (*inbytes)(R_inpstream_t, void *, int),
                     SEXP (*phook)(SEXP, SEXP), SEXP pdata);
void R_InitOutPStream(R_outpstream_t stream, R_pstream_data_t data,
                      R_pstream_format_t type, int version,
                      void (*outchar)(R_outpstream_t, int),
                      void (*outbytes)(R_outpstream_t, void *, int),
                      SEXP (*phook)(SEXP, SEXP), SEXP pdata);
```

--------------------------------

### Initialize and run R main loop (C)

Source: https://rstudio.github.io/r-manuals/r-exts/Linking-GUIs-and-other-front-ends-to-R.html

Basic C code to initialize the R interpreter and start its main event loop. This is a minimal example for embedding R.

```c
#include <Rembedded.h>

int main(int ac, char **av)
{
    /* do some setup */
    Rf_initEmbeddedR(argc, argv);
    /* do some more setup */

    /* submit some code to R, which is done interactively via
        run_Rmainloop();

        A possible substitute for a pseudo-console is

        R_ReplDLLinit();
        while(R_ReplDLLdo1() > 0) {
        /* add user actions here if desired */
       }

     */
    Rf_endEmbeddedR(0);
    /* final tidying up after R is shutdown */
    return 0;
}
```

--------------------------------

### Generate a sequence with a specific length using seq() in R

Source: https://rstudio.github.io/r-manuals/r-intro/Simple-manipulations-numbers-and-vectors.html

Use the 'length' argument in seq() to define the total number of elements in the sequence. This example generates a sequence of 51 elements starting from -5 with a step of 0.2.

```R
> s4 <- seq(length=51, from=-5, by=.2)
```

--------------------------------

### Configure R Build with Custom Settings

Source: https://rstudio.github.io/r-manuals/r-admin/Platform-notes.html

Configure the R build process using a config.site file and command-line arguments. This example sets compilers, include paths, and library paths for a shared library build with memory profiling.

```bash
CC=clang
OBJC=$CC
FC="/opt/gfortran/bin/gfortran -mtune=native"
CPPFLAGS='-isystem $LOCAL/include'
CXX=clang++
```

```bash
./configure -C \
--enable-R-shlib --enable-memory-profiling \
--x-includes=/opt/X11/include --x-libraries=/opt/X11/lib \
--with-tcl-config=$LOCAL/lib/tclConfig.sh \
--with-tk-config=$LOCAL/lib/tkConfig.sh 
PKG_CONFIG_PATH=$LOCAL/lib/pkgconfig:/usr/lib/pkgconfig
```

--------------------------------

### Rf_installTrChar

Source: https://rstudio.github.io/r-manuals/r-exts/API-index.html

Installs a translated character string as a symbol.

```APIDOC
## Rf_installTrChar

### Description
Installs a translated character string as a symbol.

### Attributes
This function is related to attributes in R.
```

--------------------------------

### Get Contiguous Data Regions from Vectors

Source: https://rstudio.github.io/r-manuals/r-exts/System-and-foreign-language-interfaces.html

These functions copy a specified number of elements (up to 'n') starting from index 'i' into a provided buffer 'buf'. The return value indicates the actual number of elements copied, which might be less than 'n'.

```c
R_xlen_t INTEGER_GET_REGION (SEXP sx, R_xlen_t i, R_xlen_t n, int *buf)
R_xlen_t LOGICAL_GET_REGION (SEXP sx, R_xlen_t i, R_xlen_t n, int *buf)
R_xlen_t REAL_GET_REGION (SEXP sx, R_xlen_t i, R_xlen_t n, double *buf)
R_xlen_t COMPLEX_GET_REGION (SEXP sx, R_xlen_t i, R_xlen_t n, Rcomplex *buf)
R_xlen_t RAW_GET_REGION (SEXP sx, R_xlen_t i, R_xlen_t n, Rbyte *buf)
```

--------------------------------

### Get linker flags using pkg-config for static R library

Source: https://rstudio.github.io/r-manuals/r-exts/Linking-GUIs-and-other-front-ends-to-R.html

Use pkg-config with the --static flag to retrieve linker flags when linking against a static R library. This may work for installed OS frameworks if pkg-config is configured.

```bash
pkg-config --static --libs libR
```

--------------------------------

### Text Connection Pushback Example

Source: https://rstudio.github.io/r-manuals/r-data/Connections.html

Demonstrates using pushBack to add lines to a text connection and then reading them. Pushbacks operate as a stack.

```r
> zz <- textConnection(LETTERS)
> readLines(zz, 2)
[1] "A" "B"
> scan(zz, "", 4)
Read 4 items
[1] "C" "D" "E" "F"
> pushBack(c("aa", "bb"), zz)
> scan(zz, "", 4)
Read 4 items
[1] "aa" "bb" "G"  "H" 
> close(zz)
```

--------------------------------

### Check an installed R package

Source: https://rstudio.github.io/r-manuals/r-exts/Creating-R-packages.html

Check an R package that has already been installed, specifying the library directory and referencing the installation log. The --install=skip option can be used if only one copy is installed.

```bash
Rdev CMD check -l libdir --install=check:pkg.log pkg
```

--------------------------------

### Configure R with Framework Support

Source: https://rstudio.github.io/r-manuals/r-admin/Platform-notes.html

Enable building R as a framework, typically for use with R.APP on macOS.

```bash
./configure --enable-R-framework
```

--------------------------------

### Running R via R CMD

Source: https://rstudio.github.io/r-manuals/r-exts/Linking-GUIs-and-other-front-ends-to-R.html

Examples of how to execute R or its components using the 'R CMD' utility, which helps set up the environment.

```shell
R CMD /usr/local/lib/R/bin/exec/R
```

```shell
R CMD exec/R
```

--------------------------------

### Build PDF and Info Manuals

Source: https://rstudio.github.io/r-manuals/r-admin/Installing-R-under-Unix-alikes.html

Use 'make pdf' to create PDF versions of the R manuals. Use 'make info' to create info files.

```makefile
make pdf      to create PDF versions
make info     to create info files (not ‘refman’ nor ‘fullrefman’).
```

--------------------------------

### Install R Packages from CRAN (R Session)

Source: https://rstudio.github.io/r-manuals/r-admin/Add-on-packages.html

Install packages from CRAN within an R session. This command will automatically fetch and install specified packages and their essential dependencies.

```r
> install.packages(c("pkg1", "pkg2"))
```

--------------------------------

### Configure and Build R

Source: https://rstudio.github.io/r-manuals/r-admin/Installing-R-under-Unix-alikes.html

Standard commands to configure and build R from source. Ensure TMPDIR is set correctly and execution is allowed.

```bash
./configure
make
```

--------------------------------

### Example of \examples section with \dontrun and \dontshow

Source: https://rstudio.github.io/r-manuals/r-exts/Writing-R-documentation-files.html

Demonstrates how to include runnable and non-runnable code in the \examples section. \dontrun{} code is shown but not executed, while \dontshow{} code is executed but not shown. Text within \dontrun{} need not be valid R code.

```r
x <- runif(10)       # Shown and run.
\dontrun{plot(x)}    # Only shown.
\dontshow{log(x)}    # Only run.
```

--------------------------------

### Install R Package to Specific Location

Source: https://rstudio.github.io/r-manuals/r-exts/Creating-R-packages.html

Use the -l option with R CMD INSTALL to specify a directory for package installation, useful for managing multiple R versions or when the default library location is not writable.

```bash
R CMD INSTALL -l location --build pkg
```

--------------------------------

### Download and Link Recommended Packages

Source: https://rstudio.github.io/r-manuals/r-admin/Obtaining-R.html

This incantation uses wget to download recommended package sources and then links them. Ensure 'dir' is set to the correct value (e.g., 'x.y.z/Recommended' or 'x.y-patched/Recommended').

```bash
wget -r -l1 --no-parent -A\*.gz -nd -P src/library/Recommended \
  https://CRAN.R-project.org/src/contrib/dir
./tools/link-recommended
```

--------------------------------

### Install Shared Objects/DLLs in R Package

Source: https://rstudio.github.io/r-manuals/r-exts/Creating-R-packages.html

This R script replicates default behavior for installing shared objects or DLLs. It copies files with the appropriate shared library extension to the 'libs' subdirectory within the package installation directory.

```r
files <- Sys.glob(paste0("*", SHLIB_EXT))
dest <- file.path(R_PACKAGE_DIR, paste0('libs', R_ARCH))
dir.create(dest, recursive = TRUE, showWarnings = FALSE)
file.copy(files, dest, overwrite = TRUE)
if(file.exists("symbols.rds"))
    file.copy("symbols.rds", dest, overwrite = TRUE)
```

--------------------------------

### Initialize R and set callbacks

Source: https://rstudio.github.io/r-manuals/r-exts/Linking-GUIs-and-other-front-ends-to-R.html

Initializes the R embedded environment, sets startup parameters, and registers custom callback functions for R's console, messages, and user interactions. Ensure R_HOME is set in the environment.

```c
R_setStartTime();
R_DefParamsEx(Rp, RSTART_VERSION);
if((RHome = get_R_HOME()) == NULL) {
    fprintf(stderr, "R_HOME must be set in the environment or Registry\n");
    exit(1);
}
Rp->rhome = RHome;
RUser = getRUser();
Rp->home = RUser;
Rp->CharacterMode = LinkDLL;
Rp->EmitEmbeddedUTF8 = FALSE;
Rp->ReadConsole = myReadConsole;
Rp->WriteConsole = myWriteConsole;
Rp->CallBack = myCallBack;
Rp->ShowMessage = askok;
Rp->YesNoCancel = askyesnocancel;
Rp->Busy = myBusy;

Rp->R_Quiet = TRUE;        /* Default is FALSE */
Rp->R_Interactive = FALSE; /* Default is TRUE */
Rp->RestoreAction = SA_RESTORE;
Rp->SaveAction = SA_NOSAVE;
R_SetParams(Rp);
freeRUser(RUser);
free_R_HOME(RHome);
R_set_command_line_arguments(argc, argv);

FlushConsoleInputBuffer(GetStdHandle(STD_INPUT_HANDLE));

signal(SIGBREAK, my_onintr);
GA_initapp(0, 0);
readconsolecfg();
setup_Rmainloop();
#ifdef SIMPLE_CASE
    run_Rmainloop();
#else
    R_ReplDLLinit();
    while(R_ReplDLLdo1() > 0) {
/* add user actions here if desired */
    }
/* only get here on EOF (not q()) */
#endif
    Rf_endEmbeddedR(0);
    return 0;
}
```

--------------------------------

### R_init Routine for Package Initialization

Source: https://rstudio.github.io/r-manuals/r-exts/System-and-foreign-language-interfaces.html

The `R_init_mypkg` function is the entry point for initializing a dynamic library. It registers routines, controls symbol visibility, and manages dynamic symbol searching.

```C
void attribute_visible R_init_mypkg(DllInfo *dll)
{
    R_registerRoutines(dll, CEntries, CallEntries, FortEntries,
                       ExternalEntries);
    R_useDynamicSymbols(dll, FALSE);
    R_forceSymbols(dll, TRUE);
...
```

--------------------------------

### Rd file header example

Source: https://rstudio.github.io/r-manuals/r-exts/Writing-R-documentation-files.html

Example of the header section in an Rd file, defining the name and aliases for documented topics.

```Rd
\name{Normal}
\alias{Normal}
\alias{dnorm}
\alias{pnorm}
\alias{qnorm}
\alias{rnorm}
```

--------------------------------

### Test R Installation Basic and Packages

Source: https://rstudio.github.io/r-manuals/r-admin/Installing-R-under-Windows.html

Launch Rgui or Rterm and execute these R commands to test basic and specific package scopes. Ensure correct locale settings for consistent results.

```R
Sys.setenv(LC_COLLATE = "C", LC_TIME="C", LANGUAGE = "en")
tools::testInstalledBasic("both")
tools::testInstalledPackages(scope = "base")
tools::testInstalledPackages(scope = "recommended")
```

--------------------------------

### Start Rterm.exe on Windows

Source: https://rstudio.github.io/r-manuals/r-intro/Invoking-R.html

On Windows command-line, 'Rterm.exe' is the preferred executable for starting R, offering a more integrated experience than 'R'.

```bash
Rterm.exe
```

--------------------------------

### Organizing Objects in Subdirectories with Make

Source: https://rstudio.github.io/r-manuals/r-exts/Creating-R-packages.html

This Makefile example shows how to organize and list object files from different subdirectories, useful for packages with complex source code structures. It defines separate variables for different categories of objects.

```makefile
OBJECTS.samplers = samplers/ExpandableArray.o samplers/Knots.o \
  samplers/RJumpSpline.o samplers/RJumpSplineFactory.o \
  samplers/RealSlicerOV.o samplers/SliceFactoryOV.o samplers/MNorm.o
OBJECTS.distributions = distributions/DSpline.o \
  distributions/DChisqrOV.o distributions/DTOV.o \
  distributions/DNormOV.o distributions/DUnifOV.o distributions/RScalarDist.o
OBJECTS.root = RJump.o

OBJECTS = $(OBJECTS.samplers) $(OBJECTS.distributions) $(OBJECTS.root)
```

--------------------------------

### Install Packages for Specific Sub-architectures

Source: https://rstudio.github.io/r-manuals/r-admin/Installing-R-under-Unix-alikes.html

To install packages for specific sub-architectures when multiple builds are present, use 'R CMD INSTALL --libs-only pkg1 pkg2 ...' with the '--arch=name' option. This is particularly useful for packages with executable configure scripts or src/Makefile.

```bash
R --arch=name CMD INSTALL --libs-only pkg1 pkg2 ...
```

--------------------------------

### 64-bit R Build Configuration for ppc64 with GCC

Source: https://rstudio.github.io/r-manuals/r-admin/Platform-notes.html

Example environment variable settings for building a 64-bit version of R on ppc64 using GCC 4.1.1. These flags are necessary for resolving linking issues with libnmath.a and building R as a shared library.

```bash
CC="gcc -m64"
CXX="gxx -m64"
FC="gfortran -m64"
CFLAGS="-mminimal-toc -fno-optimize-sibling-calls -g -O2"
FFLAGS="-mminimal-toc -fno-optimize-sibling-calls -g -O2"
```

--------------------------------

### Uninstall Shared/Static libR

Source: https://rstudio.github.io/r-manuals/r-admin/Installing-R-under-Unix-alikes.html

To uninstall a shared or static 'libR', use 'make uninstall-libR' and specify the installation prefix if it was used during installation.

```bash
make prefix=/path/to/here uninstall-libR
```

--------------------------------

### Install Binary Package on macOS

Source: https://rstudio.github.io/r-manuals/r-admin/Add-on-packages.html

On macOS, the `binary` type can be used with `install.packages` to download and install binary packages from a suitable repository.

```R
install.packages(type = "binary")
```

--------------------------------

### Configure R Build with Intel MKL

Source: https://rstudio.github.io/r-manuals/r-admin/Platform-notes.html

Set up environment variables and linker flags for using Intel Math Kernel Library (MKL) with R's configure script.

```bash
MKL_LIB_PATH=/path/to/intel_mkl/mkl/lib/intel64
export LD_LIBRARY_PATH="$MKL_LIB_PATH"
MKL="-L${MKL_LIB_PATH} -lmkl_intel_lp64 -lmkl_core -lmkl_sequential"
./configure --with-blas="$MKL" --with-lapack

```

--------------------------------

### Windows Rcmd INSTALL with Build

Source: https://rstudio.github.io/r-manuals/r-admin/Add-on-packages.html

On Windows, use the Rcmd executable for a specific architecture to install, check, and build a source package from a tarball.

```bash
.../bin/x64/Rcmd INSTALL -l libdir tarball --build > pkg.log 2>&1
```

--------------------------------

### Create an R List

Source: https://rstudio.github.io/r-manuals/r-intro/Lists-and-data-frames.html

Demonstrates how to create a list with named components of various data types.

```r
> Lst <- list(name="Fred", wife="Mary", no.children=3,
              child.ages=c(4,7,9))
```

--------------------------------

### XML Declaration Example

Source: https://rstudio.github.io/r-manuals/r-data/Introduction.html

This is an example of an XML declaration, specifying the XML version and character encoding. It is often the first line in an XML document.

```xml
<?xml version="1.0" encoding="UTF-8"?>
```

--------------------------------

### List all available pkg-config modules

Source: https://rstudio.github.io/r-manuals/r-exts/Creating-R-packages.html

Use this command to list all modules that pkg-config knows about, which can be helpful for identifying the correct module name for a library.

```bash
pkg-config --list-all | sort
```

--------------------------------

### Configure R with Sequential Intel MKL

Source: https://rstudio.github.io/r-manuals/r-admin/Essential-and-useful-other-programs-under-a-Unix-alike.html

Use this configuration for a sequential version of Intel MKL. Ensure MKL_LIB_PATH points to your MKL installation and export LD_LIBRARY_PATH.

```bash
MKL_LIB_PATH=/path/to/intel_mkl/mkl/lib/intel64
export LD_LIBRARY_PATH=$MKL_LIB_PATH
MKL="-L${MKL_LIB_PATH} -lmkl_gf_lp64 -lmkl_core -lmkl_sequential"
./configure --with-blas="$MKL" --with-lapack
```

--------------------------------

### List Files Installed by R Texinfo Component

Source: https://rstudio.github.io/r-manuals/r-admin/Installing-R-under-macOS.html

Execute this command to list all files installed by the R Texinfo component, useful for manual uninstallation.

```bash
pkgutil --files org.r-project.arm64.texinfo
```

--------------------------------

### Start R HTML Help Interface

Source: https://rstudio.github.io/r-manuals/r-intro/A-sample-session.html

Initiates the HTML interface for R's on-line help system, which opens in a web browser. It is recommended to explore the available features.

```R
help.start()
```

--------------------------------

### List Files Installed by R Tcl/Tk Component

Source: https://rstudio.github.io/r-manuals/r-admin/Installing-R-under-macOS.html

Execute this command to list all files installed by the R Tcl/Tk component, which can help in manual uninstallation.

```bash
pkgutil --files org.r-project.arm64.tcltk
```

--------------------------------

### Valgrind Configuration File

Source: https://rstudio.github.io/r-manuals/r-exts/Debugging.html

Configure Valgrind options using a configuration file for persistent settings. This is useful when using options like --use-valgrind.

```ini
--leak-check=full
--track-origins=yes
```
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