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Clearing CPPFLAGS breaks compilation in non-standard environments #10

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JeffLessem-CU opened this issue Nov 5, 2024 · 2 comments
Open

Clearing CPPFLAGS breaks compilation in non-standard environments #10

JeffLessem-CU opened this issue Nov 5, 2024 · 2 comments

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@JeffLessem-CU
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vcfppR/src/htslib-1.19.1/Makefile.vcfppR

Line 35 in adf370c

CPPFLAGS =

Resetting CPPFLAGS breaks compilation of htslib in environments with non-standard include paths, such as when R is installed under anaconda. Commenting out this line or changing it to += to allow the definition of CPPFLAGS from R CMD config CPPFLAGS to be preserved fixes the problem.
@Zilong-Li
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Thanks! Will you test it and make a PR?

@Zilong-Li
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Hey,

Can you try the new version v0.7.1, which now uses the configure script from htslib. If this doesn't work, then probably pass CPPFLAGS around is not permitted in htslib.

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@Zilong-Li @JeffLessem-CU