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SimpleITKRInstaller

Build Status CircleCI

A remotes based installer for SimpleITK in R.

Default configuration, single core compilation:

remotes::install_github("SimpleITK/SimpleITKRInstaller")

Turn on mutlicore compilation, six cores in this example

remotes::install_github("SimpleITK/SimpleITKRInstaller", configure.vars=c("MAKEJ=6"))

Use multicore compilation and build additional modules not included in the default build setup such as SimpleElastix (registration) and DCMTK (additional DICOM IO option beyond the default GDCM).

Note: We need to use backslashes to escape the spaces in the ADDITIONAL_SITK_MODULES otherwise the remotes::install does not pass the string correctly to the shell (separates it using the spaces instead of passing as one string).

remotes::install_github("SimpleITK/SimpleITKRInstaller", configure.vars=c("MAKEJ=6", "ADDITIONAL_SITK_MODULES=-DSimpleITK_USE_ELASTIX=ON\\  -DModule_ITKIODCMTK:BOOL=ON"))

Note: On Linux and Mac requires CMake and git in the path.

On Windows requires rtools installation and setting the RTOOLS_HOME environment variable. For example:

Sys.setenv(RTOOLS_HOME = "C:/rtools45")

How to Cite

If you find the R version of SimpleITK useful in your research, support our efforts by citing it as:

R. Beare, B. C. Lowekamp, Z. Yaniv, "Image Segmentation, Registration and Characterization in R with SimpleITK", J Stat Softw, 86(8), https://doi.org/10.18637/jss.v086.i08, 2018.