Linking to Rhdf5lib
25 March 2019
Package
Rhdf5lib 1.4.3
Contents
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.
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. 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 platform 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 -lfooThe 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.
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: Rhdf5libIn 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/RtmpYa7HfM/Rinst1c7164c2224c/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 3.5.3 (2019-03-11)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 16.04.6 LTS
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## Matrix products: default
## BLAS: /home/biocbuild/bbs-3.8-bioc/R/lib/libRblas.so
## LAPACK: /home/biocbuild/bbs-3.8-bioc/R/lib/libRlapack.so
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## locale:
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## [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
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## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
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## other attached packages:
## [1] BiocStyle_2.10.0
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## loaded via a namespace (and not attached):
## [1] BiocManager_1.30.4 compiler_3.5.3 magrittr_1.5
## [4] bookdown_0.9 htmltools_0.3.6 tools_3.5.3
## [7] yaml_2.2.0 Rcpp_1.0.1 stringi_1.4.3
## [10] rmarkdown_1.12 knitr_1.22 stringr_1.4.0
## [13] digest_0.6.18 xfun_0.5 evaluate_0.13