# Linking to Rhdf5lib
Date: 2024-05-01

Mike L. Smith1

1de.NBI & EMBL Heidelberg

#### 1 May 2024

#### Package

Rhdf5lib 1.26.0

# Contents

# 1 Motivation

Rhdf5lib provides versions of the C and C++ HDF5 libraries. It is primarily useful to developers of other R packages who want to make use of the capabilities of the HDF5 library directly in the C or C++ code of their own packages, rather than using a higher level interface such as the rhdf5 package. Using Rhdf5lib makes life easier for users, as they do not have to worry about installing libraries at a system level, and for developers since they can work with a defined version of the library rather than developing strategies to cope with the potential for multiple versions.

Rhdf5lib is very much inspired by the zlibbioc and Rhtslib packages.

# 2 Usage

There is an example package, usingRhdf5lib, that demonstrates how packages should link to Rhdf5lib.

## 2.1 Link to the library

To link successfully to the HDF5 library included in Rhdf5lib a package must include both a `src/Makevars.win` and `src/Makevars` file.

Add the following lines to both `src/Makevars` and `src/Makevars.win`

    RHDF5_LIBS=$(shell "${R_HOME}/bin${R_ARCH_BIN}/Rscript" -e \
        'Rhdf5lib::pkgconfig("PKG_C_LIBS")')
    PKG_LIBS=$(RHDF5_LIBS)

The statement for each platform modifies the `$PKG_LIBS` variable. If your package needs to add additional information to the `$PKG_LIBS` variable, do so by adding to the `PKG_LIBS=$(RHDF5_LIBS)` line, e.g.,

    PKG_LIBS=$(RHDF5_LIBS) -L/path/to/foolib -lfoo

Note that the use of `$(shell ...)` necessitates using GNU Make, and you need to make this requirement explicit in your package’s DESCRIPTION file via the entry:

    SystemRequirements: GNU make

The default behaviour of `Rhdf5lib::pkgconfig` is to report the location of the shared library as the result of `system.file("lib", package="Rhdf5lib")`. If this is inappropriate for your system e.g. a cluster with a shared file system, use the environment variable `RHDF5LIB_RPATH` to override this and set an appropriate location for your infrastructure.

Valid options to provide to `pkgconfig()` are: `PKG_C_LIBS`, `PKG_CXX_LIBS`, `PKG_C_HL_LIBS` and `PKG_CXX_HL_LIBS`. Choose the most appropriate depending upon whether your linking code requires the C++ API (`C` vs `CXX`) and/or the HDF5 ‘high-level’ API (`HL`). Choosing options that you don’t require should not harm performance, but will result in a larger library and potentially greater memory usage for your application, so it is good practice to select only the features you need.

## 2.2 Locating the library headers

In order for the C/C++ compiler to find the HDF5 headers during package installation, add Rhdf5lib to the LinkingTo field of the DESCRIPTION file of your package, e.g.

    LinkingTo: Rhdf5lib

In you C or C++ code files, you can then use the standard include techniques, e.g., `#include "hdf5.h"` or `#include "H5Cpp.h"`. You can inspect the header files manually to check their names and declared functions. To find their location on your system you can use the following code:

    system.file(package="Rhdf5lib", "include")

    ## [1] "/tmp/Rtmpt5LIlx/Rinst44e6699a1de/Rhdf5lib/include"

# 3 Configuration arguments for non-standard system setups

## 3.1 Non-standard ZLIB location

Rhdf5lib requires the ZLIB compression library to be installed on non-Windows platforms. If installation fails with a message reporting that zlib.h can not be found, it is possible to provide the appropriate path explicitly during installation via the `configure.args` argument e.g.

    BiocManager::install('Rhdf5lib', configure.args = "--with-zlib='/path/to/zlib/'")

Here `/path/to/zlib` should be the directory that contains both `include/zlib.h` and `lib/libz.a`. For example, on a typical Ubuntu installation this may be `/usr/` while for libraries installed via miniconda this location could be `/home/<USER>/miniconda3/`.

## 3.2 Disabling link time optimisation (LTO)

If you have configured R with link-time optimisation enabled (see here), but wish to turn it off for the installation of Rhdf5lib, you need to set both the `configure.args` and `INSTALL_opts` arguments e.g.

    BiocManager::install('Rhdf5lib', INSTALL_opts="--no-use-LTO", configure.args = "--disable-lto")

This is because building Rhdf5lib involves first compiling the HDF5 library, and then compiling and linking the R interface against that. The `INSTALL_opts` argument affects the latter part, but we need to use `configure.args` to ensure the HDF5 library is built with the same settings. 11 1 Using `"--enable-lto"` here will have no effect. To enable link-time optimisation you must have already configured R with `--enable-lto` (see here).

## 3.3 Disabling setting rpath

If you encounter problems checking whether to use `-Wl,-rpath` to “link shared libs in nondefault directories” you can disable the test by passing the option `"--disable-sharedlib-rath"` to the configuration script.

    BiocManager::install('Rhdf5lib', configure.args = "--disable-sharedlib-rath")

# 4 Funding

MLS was supported by the BMBF-funded Heidelberg Center for Human Bioinformatics (HD-HuB) within the German Network for Bioinformatics Infrastructure (de.NBI), Grant Number #031A537B

# Session info

    ## R version 4.4.0 beta (2024-04-15 r86425)
    ## Platform: x86_64-pc-linux-gnu
    ## Running under: Ubuntu 22.04.4 LTS
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    ## BLAS:   /home/biocbuild/bbs-3.19-bioc/R/lib/libRblas.so
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    ## attached base packages:
    ## [1] stats     graphics  grDevices utils     datasets  methods   base
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    ## other attached packages:
    ## [1] BiocStyle_2.32.0
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