1 Motivation
2 Usage
- 2.1 Link to the library
- 2.2 Locating the library headers
3 Funding
Session info

1 Motivation

Rhdf5lib provides 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 make 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.

Rhdf5 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. Note: the contents of src/Makevars.win and src/Makevars are almost identical, but not quite. Be careful of the differences.

Create a src/Makevars.win file with the following lines

RHDF5_LIBS=$(shell echo 'Rhdf5lib::pkgconfig("PKG_CXX_LIBS")'|\
    "${R_HOME}/bin/R" --vanilla --slave)  
PKG_LIBS=$(RHDF5_LIBS)

and a src/Makevars file with the following lines

RHDF5_LIBS=`echo 'Rhdf5lib::pkgconfig("PKG_CXX_LIBS")'|\
    "${R_HOME}/bin/R" --vanilla --slave`
PKG_LIBS=$(RHDF5_LIBS)

The statement for each platfrom modifies the $PKG_LIBS variable. If your package needs to add 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

2.2 Locating the library headers

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

LinkingTo: Rhtslib

In you C or C++ code files, you can then use the standard include techniques, e.g., #include "hdf5.h" or #include "c++/hdf5.h". C header files do not need a subfolder specified, while C++ headers are located under c++. 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/RtmpFSRrIL/Rinst15b1695bb59d/Rhdf5lib/include"

3 Funding

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

Session info

## R version 3.4.2 (2017-09-28)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 16.04.3 LTS
## 
## Matrix products: default
## BLAS: /home/biocbuild/bbs-3.6-bioc/R/lib/libRblas.so
## LAPACK: /home/biocbuild/bbs-3.6-bioc/R/lib/libRlapack.so
## 
## locale:
##  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
##  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=C              
##  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
##  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
##  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
## [1] BiocStyle_2.6.0
## 
## loaded via a namespace (and not attached):
##  [1] compiler_3.4.2  backports_1.1.1 bookdown_0.5    magrittr_1.5   
##  [5] rprojroot_1.2   htmltools_0.3.6 tools_3.4.2     yaml_2.1.14    
##  [9] Rcpp_0.12.13    stringi_1.1.5   rmarkdown_1.6   knitr_1.17     
## [13] stringr_1.2.0   digest_0.6.12   evaluate_0.10.1

Linking to Rhdf5lib

30 October 2017

Package

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