New variables to find external packages - Githubissues

Bioconductor / Rhtslib

HTSlib high-throughput sequencing library as an R package

https://bioconductor.org/packages/Rhtslib

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New variables to find external packages #17

Closed glennpj closed 4 years ago

glennpj commented 4 years ago

When trying to build Rhtslib in spack, the spack built bzip2 and xz packages could not be found when the internal htslib was built. This PR adds a couple of environment variables that can be used to define the locations of bzip2 and xz.

BZIP2_INCLUDE and XZ_INCLUDE: Can be set like CPPFLAGS, '-I/path/to/package/include'
BZIP2_LIB and XZ_LIB: Can be set like LDFLAGS, `-L/path/to/lib'

A PR for spack that implements this is https://github.com/spack/spack/pull/14863

This change, or similar, might be useful for other build environments as well.

hpages commented 4 years ago

Rhtslib inherits LDFLAGS from R and R should "know" about the location of the bzip2 and xz libraries. If it doesn't then it's not properly configured. See https://github.com/Bioconductor/Rhtslib/issues/12