Skip to content

Commit 5ac440f

Browse files
committed
Ensure -I./htslib takes priority over /usr/local/include
We need to search /usr/local/include to find curl/curl.h etc. However it needs to be searched AFTER ./htslib et al so that pysam is compiled against headers from ./htslib/htslib/*.h rather than any system-installed HTSlib headers in /usr/local/include.
1 parent bfa5a41 commit 5ac440f

File tree

1 file changed

+1
-1
lines changed

1 file changed

+1
-1
lines changed

.cirrus.yml

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -8,7 +8,7 @@ freebsd_ci_task:
88
pkg install -y bcftools gmake py311-cython3 py311-mypy py311-pytest samtools
99
1010
env:
11-
CC: "clang -I/usr/local/include"
11+
CC: "clang -isystem /usr/local/include"
1212
MAKE: "gmake"
1313
REF_PATH: ":"
1414

0 commit comments

Comments
 (0)