Skip to content

MinGW support#1400

Open
theAeon wants to merge 16 commits into
pysam-developers:masterfrom
theAeon:pysam-mingw
Open

MinGW support#1400
theAeon wants to merge 16 commits into
pysam-developers:masterfrom
theAeon:pysam-mingw

build for windows

1b60783
Select commit
Loading
Failed to load commit list.
Cirrus CI / CI / FreeBSD failed Mar 24, 2026 in 1m 7s

Task Summary

Instruction build failed in 00:38

Details

⚠️ Not enough compute credits to prioritize tasks!

✅ 00:05 clone
✅ 00:21 install
❌ 00:38 build

 3527 |                             if (0 && CRAM_MAJOR_VERS(fd->version) >= 3) {
      |                                 ^
      |                                 /* DISABLES CODE */ ( )
cram/cram_encode.c:3491:17: warning: code will never be executed [-Wunreachable-code]
 3491 |                 int l;
      |                 ^~~~~~
3 warnings generated.
clang -isystem /usr/local/include -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe  -fstack-protector-strong -fno-strict-aliasing -fPIC -fvisibility=hidden  -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement   -c -o cram/cram_external.o cram/cram_external.c
clang -isystem /usr/local/include -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe  -fstack-protector-strong -fno-strict-aliasing -fPIC -fvisibility=hidden  -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement   -c -o cram/cram_index.o cram/cram_index.c
clang -isystem /usr/local/include -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe  -fstack-protector-strong -fno-strict-aliasing -fPIC -fvisibility=hidden  -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement   -c -o cram/cram_io.o cram/cram_io.c
clang -isystem /usr/local/include -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe  -fstack-protector-strong -fno-strict-aliasing -fPIC -fvisibility=hidden  -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement   -c -o cram/cram_stats.o cram/cram_stats.c
clang -isystem /usr/local/include -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe  -fstack-protector-strong -fno-strict-aliasing -fPIC -fvisibility=hidden  -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement   -c -o cram/mFILE.o cram/mFILE.c
clang -isystem /usr/local/include -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe  -fstack-protector-strong -fno-strict-aliasing -fPIC -fvisibility=hidden  -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement   -c -o cram/open_trace_file.o cram/open_trace_file.c
clang -isystem /usr/local/include -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe  -fstack-protector-strong -fno-strict-aliasing -fPIC -fvisibility=hidden  -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement   -c -o cram/pooled_alloc.o cram/pooled_alloc.c
clang -isystem /usr/local/include -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe  -fstack-protector-strong -fno-strict-aliasing -fPIC -fvisibility=hidden  -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement   -c -o cram/string_alloc.o cram/string_alloc.c
clang -isystem /usr/local/include -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe  -fstack-protector-strong -fno-strict-aliasing -fPIC -fvisibility=hidden  -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement   -c -o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/arith_dynamic.c
htscodecs/htscodecs/arith_dynamic.c:191:14: warning: code will never be executed [-Wunreachable-code]
  191 |     if (1 || in_size > 1000) {
      |              ^~~~~~~
htscodecs/htscodecs/arith_dynamic.c:191:9: note: silence by adding parentheses to mark code as explicitly dead
  191 |     if (1 || in_size > 1000) {
      |         ^
      |         /* DISABLES CODE */ ( )
1 warning generated.
clang -isystem /usr/local/include -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe  -fstack-protector-strong -fno-strict-aliasing -fPIC -fvisibility=hidden  -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement   -c -o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/fqzcomp_qual.c
clang -isystem /usr/local/include -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe  -fstack-protector-strong -fno-strict-aliasing -fPIC -fvisibility=hidden  -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement   -c -o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/htscodecs.c
clang -isystem /usr/local/include -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe  -fstack-protector-strong -fno-strict-aliasing -fPIC -fvisibility=hidden  -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement   -c -o htscodecs/htscodecs/pack.o htscodecs/htscodecs/pack.c
clang -isystem /usr/local/include -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe  -fstack-protector-strong -fno-strict-aliasing -fPIC -fvisibility=hidden  -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement   -c -o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_static4x16pr.c
clang -isystem /usr/local/include -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe  -fstack-protector-strong -fno-strict-aliasing -fPIC -fvisibility=hidden -mavx2 -mpopcnt -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement   -c -o htscodecs/htscodecs/rANS_static32x16pr_avx2.o htscodecs/htscodecs/rANS_static32x16pr_avx2.c
htscodecs/htscodecs/rANS_static32x16pr_avx2.c:1120:9: warning: code will never be executed [-Wunreachable-code]
 1120 |         int z;
      |         ^~~~~~
htscodecs/htscodecs/rANS_static32x16pr_avx2.c:1119:9: note: silence by adding parentheses to mark code as explicitly dead
 1119 |     if (0) {
      |         ^
      |         /* DISABLES CODE */ ( )
1 warning generated.
clang -isystem /usr/local/include -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe  -fstack-protector-strong -fno-strict-aliasing -fPIC -fvisibility=hidden -mavx512f -mpopcnt -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement   -c -o htscodecs/htscodecs/rANS_static32x16pr_avx512.o htscodecs/htscodecs/rANS_static32x16pr_avx512.c
clang -isystem /usr/local/include -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe  -fstack-protector-strong -fno-strict-aliasing -fPIC -fvisibility=hidden -msse4.1 -mssse3 -mpopcnt -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement   -c -o htscodecs/htscodecs/rANS_static32x16pr_sse4.o htscodecs/htscodecs/rANS_static32x16pr_sse4.c
clang -isystem /usr/local/include -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe  -fstack-protector-strong -fno-strict-aliasing -fPIC -fvisibility=hidden  -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement   -c -o htscodecs/htscodecs/rANS_static32x16pr_neon.o htscodecs/htscodecs/rANS_static32x16pr_neon.c
clang -isystem /usr/local/include -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe  -fstack-protector-strong -fno-strict-aliasing -fPIC -fvisibility=hidden  -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement   -c -o htscodecs/htscodecs/rANS_static32x16pr.o htscodecs/htscodecs/rANS_static32x16pr.c
clang -isystem /usr/local/include -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe  -fstack-protector-strong -fno-strict-aliasing -fPIC -fvisibility=hidden  -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement   -c -o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rANS_static.c
clang -isystem /usr/local/include -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe  -fstack-protector-strong -fno-strict-aliasing -fPIC -fvisibility=hidden  -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement   -c -o htscodecs/htscodecs/rle.o htscodecs/htscodecs/rle.c
clang -isystem /usr/local/include -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe  -fstack-protector-strong -fno-strict-aliasing -fPIC -fvisibility=hidden  -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement   -c -o htscodecs/htscodecs/tokenise_name3.o htscodecs/htscodecs/tokenise_name3.c
clang -isystem /usr/local/include -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe  -fstack-protector-strong -fno-strict-aliasing -fPIC -fvisibility=hidden  -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement   -c -o htscodecs/htscodecs/utils.o htscodecs/htscodecs/utils.c
clang -isystem /usr/local/include -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe  -fstack-protector-strong -fno-strict-aliasing -fPIC -fvisibility=hidden  -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement   -c -o hfile_libcurl.o hfile_libcurl.c
clang -isystem /usr/local/include -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe  -fstack-protector-strong -fno-strict-aliasing -fPIC -fvisibility=hidden  -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement   -c -o hfile_gcs.o hfile_gcs.c
clang -isystem /usr/local/include -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe  -fstack-protector-strong -fno-strict-aliasing -fPIC -fvisibility=hidden  -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement   -c -o hfile_s3.o hfile_s3.c
ar -rc libhts.a kfunc.o kstring.o bcf_sr_sort.o bgzf.o errmod.o faidx.o header.o hfile.o hts.o hts_expr.o hts_os.o md5.o multipart.o probaln.o realn.o regidx.o region.o sam.o sam_mods.o simd.o synced_bcf_reader.o vcf_sweep.o tbx.o textutils.o thread_pool.o vcf.o vcfutils.o cram/cram_codecs.o cram/cram_decode.o cram/cram_encode.o cram/cram_external.o cram/cram_index.o cram/cram_io.o cram/cram_stats.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/string_alloc.o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/pack.o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_static32x16pr_avx2.o htscodecs/htscodecs/rANS_static32x16pr_avx512.o htscodecs/htscodecs/rANS_static32x16pr_sse4.o htscodecs/htscodecs/rANS_static32x16pr_neon.o htscodecs/htscodecs/rANS_static32x16pr.o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rle.o htscodecs/htscodecs/tokenise_name3.o htscodecs/htscodecs/utils.o  hfile_libcurl.o hfile_gcs.o hfile_s3.o
ranlib libhts.a
Compiling pysam/libchtslib.pyx because it changed.
[1/1] Cythonizing pysam/libchtslib.pyx
building 'pysam.libchtslib' extension
clang -isystem /usr/local/include -mdll -O -Wall -I/tmp/cirrus-ci-build/pysam -I/tmp/cirrus-ci-build/htslib -I/tmp/cirrus-ci-build/samtools -I/tmp/cirrus-ci-build/samtools/lz4 -I/tmp/cirrus-ci-build/bcftools -I/tmp/cirrus-ci-build -I/usr/local/include/python3.11 -c pysam/htslib_util.c -o build/temp.freebsd-15.0-RELEASE-amd64-cpython-311/pysam/htslib_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
clang: error: unsupported option '-mdll' for target 'x86_64-unknown-freebsd15.0'
error: command '/usr/bin/clang' failed with exit code 1