Sep 10 10:45:40.939 INFO checking rust-htslib-0.21.0 against master#f50b7758f4dc85dc1c5e38258adaa94213ac6ed1 for pr-54090 Sep 10 10:45:40.939 INFO running: cargo +f50b7758f4dc85dc1c5e38258adaa94213ac6ed1-alt check --frozen --all --all-targets Sep 10 10:45:40.939 INFO running `"docker" "create" "-v" "/home/ec2-user/crater/./work/local/test-source/worker-2/pr-54090/master#f50b7758f4dc85dc1c5e38258adaa94213ac6ed1:/source:ro,Z" "-v" "/home/ec2-user/crater/./work/local/target-dirs/pr-54090/worker-2/master#f50b7758f4dc85dc1c5e38258adaa94213ac6ed1:/target:rw,Z" "-v" "/home/ec2-user/crater/./work/local/cargo-home:/cargo-home:ro,Z" "-v" "/home/ec2-user/crater/./work/local/rustup-home:/rustup-home:ro,Z" "-e" "USER_ID=1000" "-e" "CMD=cargo +f50b7758f4dc85dc1c5e38258adaa94213ac6ed1-alt check --frozen --all --all-targets" "-e" "CARGO_INCREMENTAL=0" "-e" "RUST_BACKTRACE=full" "-e" "RUSTFLAGS=--cap-lints=warn" "-m" "2G" "crater"` Sep 10 10:45:41.292 INFO blam! 4f7702c689583b2bc9a80de27228347d19475cf1462b90577019988426310733 Sep 10 10:45:41.294 INFO running `"docker" "start" "-a" "4f7702c689583b2bc9a80de27228347d19475cf1462b90577019988426310733"` Sep 10 10:45:42.386 INFO kablam! usermod: no changes Sep 10 10:45:42.724 INFO kablam! Compiling bindgen v0.36.1 Sep 10 10:45:42.724 INFO kablam! Checking ieee754 v0.2.2 Sep 10 10:45:42.724 INFO kablam! Checking linear-map v1.2.0 Sep 10 10:45:42.730 INFO kablam! Compiling clang-sys v0.22.0 Sep 10 10:45:42.738 INFO kablam! Compiling fs-utils v1.1.0 Sep 10 10:45:42.742 INFO kablam! Checking bio-types v0.2.0 Sep 10 10:46:11.340 INFO kablam! Compiling rust-htslib v0.21.0 (file:///source) Sep 10 10:46:31.933 INFO kablam! error: failed to run custom build command for `rust-htslib v0.21.0 (file:///source)` Sep 10 10:46:31.933 INFO kablam! process didn't exit successfully: `/target/debug/build/rust-htslib-f55fd41c61d31c02/build-script-build` (exit code: 101) Sep 10 10:46:31.933 INFO kablam! --- stdout Sep 10 10:46:31.933 INFO kablam! echo '/* Default config.h generated by Makefile */' > config.h Sep 10 10:46:31.933 INFO kablam! echo '#define HAVE_LIBBZ2 1' >> config.h Sep 10 10:46:31.933 INFO kablam! echo '#define HAVE_LIBLZMA 1' >> config.h Sep 10 10:46:31.933 INFO kablam! echo '#define HAVE_FSEEKO 1' >> config.h Sep 10 10:46:31.933 INFO kablam! echo '#define HAVE_DRAND48 1' >> config.h Sep 10 10:46:31.933 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o kfunc.o kfunc.c Sep 10 10:46:31.933 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o knetfile.o knetfile.c Sep 10 10:46:31.933 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o kstring.o kstring.c Sep 10 10:46:31.933 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o bcf_sr_sort.o bcf_sr_sort.c Sep 10 10:46:31.933 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o bgzf.o bgzf.c Sep 10 10:46:31.933 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o errmod.o errmod.c Sep 10 10:46:31.933 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o faidx.o faidx.c Sep 10 10:46:31.933 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o hfile.o hfile.c Sep 10 10:46:31.933 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o hfile_net.o hfile_net.c Sep 10 10:46:31.933 INFO kablam! echo '#define HTS_VERSION "1.6"' > version.h Sep 10 10:46:31.933 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o hts.o hts.c Sep 10 10:46:31.933 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o hts_os.o hts_os.c Sep 10 10:46:31.933 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o md5.o md5.c Sep 10 10:46:31.933 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o multipart.o multipart.c Sep 10 10:46:31.933 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o probaln.o probaln.c Sep 10 10:46:31.933 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o realn.o realn.c Sep 10 10:46:31.933 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o regidx.o regidx.c Sep 10 10:46:31.933 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o sam.o sam.c Sep 10 10:46:31.933 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o synced_bcf_reader.o synced_bcf_reader.c Sep 10 10:46:31.933 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o vcf_sweep.o vcf_sweep.c Sep 10 10:46:31.933 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o tbx.o tbx.c Sep 10 10:46:31.933 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o textutils.o textutils.c Sep 10 10:46:31.933 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o thread_pool.o thread_pool.c Sep 10 10:46:31.933 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o vcf.o vcf.c Sep 10 10:46:31.933 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o vcfutils.o vcfutils.c Sep 10 10:46:31.933 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o cram/cram_codecs.o cram/cram_codecs.c Sep 10 10:46:31.933 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o cram/cram_decode.o cram/cram_decode.c Sep 10 10:46:31.933 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o cram/cram_encode.o cram/cram_encode.c Sep 10 10:46:31.933 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o cram/cram_external.o cram/cram_external.c Sep 10 10:46:31.933 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o cram/cram_index.o cram/cram_index.c Sep 10 10:46:31.933 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o cram/cram_io.o cram/cram_io.c Sep 10 10:46:31.933 INFO kablam! Makefile:120: recipe for target 'cram/cram_io.o' failed Sep 10 10:46:31.933 INFO kablam! Sep 10 10:46:31.933 INFO kablam! --- stderr Sep 10 10:46:31.933 INFO kablam! cram/cram_io.c:57:19: fatal error: bzlib.h: No such file or directory Sep 10 10:46:31.933 INFO kablam! compilation terminated. Sep 10 10:46:31.933 INFO kablam! make: *** [cram/cram_io.o] Error 1 Sep 10 10:46:31.933 INFO kablam! thread 'main' panicked at 'failed to build htslib', build.rs:59:9 Sep 10 10:46:31.933 INFO kablam! stack backtrace: Sep 10 10:46:31.934 INFO kablam! 0: 0x5562f96f530e - std::sys::unix::backtrace::tracing::imp::unwind_backtrace::hd1ddf909c3007e6f Sep 10 10:46:31.934 INFO kablam! at libstd/sys/unix/backtrace/tracing/gcc_s.rs:49 Sep 10 10:46:31.934 INFO kablam! 1: 0x5562f96e4486 - std::sys_common::backtrace::print::h8af87ee7033cea48 Sep 10 10:46:31.934 INFO kablam! at libstd/sys_common/backtrace.rs:71 Sep 10 10:46:31.934 INFO kablam! at libstd/sys_common/backtrace.rs:59 Sep 10 10:46:31.934 INFO kablam! 2: 0x5562f96e280d - std::panicking::default_hook::{{closure}}::hb070ea60f8cf9536 Sep 10 10:46:31.934 INFO kablam! at libstd/panicking.rs:211 Sep 10 10:46:31.934 INFO kablam! 3: 0x5562f96e2580 - std::panicking::default_hook::h108b3d1da16fc0ff Sep 10 10:46:31.934 INFO kablam! at libstd/panicking.rs:227 Sep 10 10:46:31.934 INFO kablam! 4: 0x5562f96e2e7c - std::panicking::rust_panic_with_hook::he22c3c9d0a2321e8 Sep 10 10:46:31.934 INFO kablam! at libstd/panicking.rs:477 Sep 10 10:46:31.934 INFO kablam! 5: 0x5562f951d61f - std::panicking::begin_panic::h0295466bcb96d22d Sep 10 10:46:31.934 INFO kablam! at /checkout/src/libstd/panicking.rs:411 Sep 10 10:46:31.934 INFO kablam! 6: 0x5562f9108454 - build_script_build::main::hc6ac7db079e2de02 Sep 10 10:46:31.934 INFO kablam! at /source/build.rs:59 Sep 10 10:46:31.934 INFO kablam! 7: 0x5562f910957f - std::rt::lang_start::{{closure}}::h0540773a4cd1e12b Sep 10 10:46:31.934 INFO kablam! at /checkout/src/libstd/rt.rs:74 Sep 10 10:46:31.934 INFO kablam! 8: 0x5562f96e2912 - std::panicking::try::do_call::hd17f7bbbc80cfc74 Sep 10 10:46:31.934 INFO kablam! at libstd/rt.rs:59 Sep 10 10:46:31.934 INFO kablam! at libstd/panicking.rs:310 Sep 10 10:46:31.934 INFO kablam! 9: 0x5562f9707a29 - __rust_maybe_catch_panic Sep 10 10:46:31.934 INFO kablam! at libpanic_unwind/lib.rs:103 Sep 10 10:46:31.934 INFO kablam! 10: 0x5562f96efcf5 - std::rt::lang_start_internal::h8194e5e3064ac4bd Sep 10 10:46:31.934 INFO kablam! at libstd/panicking.rs:289 Sep 10 10:46:31.934 INFO kablam! at libstd/panic.rs:392 Sep 10 10:46:31.934 INFO kablam! at libstd/rt.rs:58 Sep 10 10:46:31.934 INFO kablam! 11: 0x5562f9109557 - std::rt::lang_start::h384c5ae564ca7a58 Sep 10 10:46:31.934 INFO kablam! at /checkout/src/libstd/rt.rs:74 Sep 10 10:46:31.934 INFO kablam! 12: 0x5562f9108919 - main Sep 10 10:46:31.934 INFO kablam! 13: 0x7fa1e8ee182f - __libc_start_main Sep 10 10:46:31.934 INFO kablam! 14: 0x5562f9107b08 - _start Sep 10 10:46:31.934 INFO kablam! 15: 0x0 - Sep 10 10:46:31.934 INFO kablam! Sep 10 10:46:31.934 INFO kablam! su: No module specific data is present Sep 10 10:46:32.446 INFO running `"docker" "rm" "-f" "4f7702c689583b2bc9a80de27228347d19475cf1462b90577019988426310733"` Sep 10 10:46:32.498 INFO blam! 4f7702c689583b2bc9a80de27228347d19475cf1462b90577019988426310733