Clearing CPPFLAGS breaks compilation in non-standard environments

Zilong-Li / vcfppR

The fastest VCF/BCF parser in R https://doi.org/10.1093/bioinformatics/btae049

https://zilong-li.github.io/vcfppR/

Other

13 stars 3 forks source link

Clearing CPPFLAGS breaks compilation in non-standard environments #10

Open JeffLessem-CU opened 1 week ago

JeffLessem-CU commented 1 week ago

https://github.com/Zilong-Li/vcfppR/blob/adf370c3a474a7ea66301f0523f16ee2cae78434/src/htslib-1.19.1/Makefile.vcfppR#L35

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 commented 1 week ago

Thanks! Will you test it and make a PR?