Linking to Rhdf5lib

Mike L. Smith1

1de.NBI & EMBL Heidelberg

Package

Rhdf5lib 1.16.0

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 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/Rtmpgh1Ipv/Rinst1c846f5bd7f1df/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. 111 Using "--enable-lto" here will have no effect. To enable link-time optimisation you must have already configured R with --enable-lto (see here).

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 4.1.1 (2021-08-10)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 20.04.3 LTS
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## Matrix products: default
## BLAS:   /home/biocbuild/bbs-3.14-bioc/R/lib/libRblas.so
## LAPACK: /home/biocbuild/bbs-3.14-bioc/R/lib/libRlapack.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_2.22.0
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##  [1] bookdown_0.24       digest_0.6.28       R6_2.5.1           
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## [10] bslib_0.3.1         rmarkdown_2.11      tools_4.1.1        
## [13] stringr_1.4.0       xfun_0.27           yaml_2.2.1         
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