Aug 11 03:24:03.256 INFO checking rust-htslib-0.21.0 against master#f6d43ed84207c7e58f363f46e5a438ff40f2b311 for libc-1 Aug 11 03:24:03.257 INFO running: cargo +f6d43ed84207c7e58f363f46e5a438ff40f2b311-alt check --frozen --all --all-targets Aug 11 03:24:03.257 INFO creating container for: cargo +f6d43ed84207c7e58f363f46e5a438ff40f2b311-alt check --frozen --all --all-targets Aug 11 03:24:03.258 INFO running `"docker" "create" "-v" "/tmp/crater.M2x8Q0qcCxt3:/source:ro,Z" "-v" "/home/ec2-user/crater/./work/local/target-dirs/libc-1/worker-1/master#f6d43ed84207c7e58f363f46e5a438ff40f2b311:/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" "-v" "/home/ec2-user/crater/./work/local/cargo-home/git:/cargo-home/git:rw,Z" "-e" "USER_ID=500" "-e" "CMD=cargo +f6d43ed84207c7e58f363f46e5a438ff40f2b311-alt check --frozen --all --all-targets" "-e" "CARGO_INCREMENTAL=0" "-e" "RUST_BACKTRACE=full" "-e" "RUSTFLAGS=--cap-lints=warn" "crater"` Aug 11 03:24:03.507 INFO blam! 0df56f42cc77d8e2a9df69e6594d00a4d12452393f0f556f5ccfb4e9e589d93d Aug 11 03:24:03.509 INFO running `"docker" "start" "-a" "0df56f42cc77d8e2a9df69e6594d00a4d12452393f0f556f5ccfb4e9e589d93d"` Aug 11 03:24:04.920 INFO kablam! Compiling bindgen v0.36.1 Aug 11 03:24:04.922 INFO kablam! Checking ieee754 v0.2.2 Aug 11 03:24:04.922 INFO kablam! Checking linear-map v1.2.0 Aug 11 03:24:04.926 INFO kablam! Compiling clang-sys v0.22.0 Aug 11 03:24:04.926 INFO kablam! Compiling fs-utils v1.1.0 Aug 11 03:24:04.933 INFO kablam! Compiling newtype_derive v0.1.6 Aug 11 03:24:04.940 INFO kablam! Checking bio-types v0.2.0 Aug 11 03:25:03.965 INFO kablam! Compiling rust-htslib v0.21.0 (file:///source) Aug 11 03:25:38.170 INFO kablam! error: failed to run custom build command for `rust-htslib v0.21.0 (file:///source)` Aug 11 03:25:38.171 INFO kablam! process didn't exit successfully: `/target/debug/build/rust-htslib-42f8fb4d59e1fd9c/build-script-build` (exit code: 101) Aug 11 03:25:38.171 INFO kablam! --- stdout Aug 11 03:25:38.171 INFO kablam! echo '/* Default config.h generated by Makefile */' > config.h Aug 11 03:25:38.171 INFO kablam! echo '#define HAVE_LIBBZ2 1' >> config.h Aug 11 03:25:38.171 INFO kablam! echo '#define HAVE_LIBLZMA 1' >> config.h Aug 11 03:25:38.171 INFO kablam! echo '#define HAVE_FSEEKO 1' >> config.h Aug 11 03:25:38.171 INFO kablam! echo '#define HAVE_DRAND48 1' >> config.h Aug 11 03:25:38.171 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o kfunc.o kfunc.c Aug 11 03:25:38.171 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o knetfile.o knetfile.c Aug 11 03:25:38.171 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o kstring.o kstring.c Aug 11 03:25:38.171 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o bcf_sr_sort.o bcf_sr_sort.c Aug 11 03:25:38.171 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o bgzf.o bgzf.c Aug 11 03:25:38.171 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o errmod.o errmod.c Aug 11 03:25:38.171 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o faidx.o faidx.c Aug 11 03:25:38.171 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o hfile.o hfile.c Aug 11 03:25:38.171 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o hfile_net.o hfile_net.c Aug 11 03:25:38.171 INFO kablam! echo '#define HTS_VERSION "1.6"' > version.h Aug 11 03:25:38.171 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o hts.o hts.c Aug 11 03:25:38.171 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o hts_os.o hts_os.c Aug 11 03:25:38.171 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o md5.o md5.c Aug 11 03:25:38.171 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o multipart.o multipart.c Aug 11 03:25:38.171 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o probaln.o probaln.c Aug 11 03:25:38.171 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o realn.o realn.c Aug 11 03:25:38.171 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o regidx.o regidx.c Aug 11 03:25:38.171 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o sam.o sam.c Aug 11 03:25:38.172 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o synced_bcf_reader.o synced_bcf_reader.c Aug 11 03:25:38.172 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o vcf_sweep.o vcf_sweep.c Aug 11 03:25:38.172 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o tbx.o tbx.c Aug 11 03:25:38.172 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o textutils.o textutils.c Aug 11 03:25:38.172 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o thread_pool.o thread_pool.c Aug 11 03:25:38.172 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o vcf.o vcf.c Aug 11 03:25:38.172 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o vcfutils.o vcfutils.c Aug 11 03:25:38.172 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o cram/cram_codecs.o cram/cram_codecs.c Aug 11 03:25:38.172 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o cram/cram_decode.o cram/cram_decode.c Aug 11 03:25:38.172 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o cram/cram_encode.o cram/cram_encode.c Aug 11 03:25:38.172 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o cram/cram_external.o cram/cram_external.c Aug 11 03:25:38.172 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o cram/cram_index.o cram/cram_index.c Aug 11 03:25:38.172 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o cram/cram_io.o cram/cram_io.c Aug 11 03:25:38.172 INFO kablam! Makefile:120: recipe for target 'cram/cram_io.o' failed Aug 11 03:25:38.172 INFO kablam! Aug 11 03:25:38.172 INFO kablam! --- stderr Aug 11 03:25:38.172 INFO kablam! cram/cram_io.c:57:19: fatal error: bzlib.h: No such file or directory Aug 11 03:25:38.172 INFO kablam! compilation terminated. Aug 11 03:25:38.172 INFO kablam! make: *** [cram/cram_io.o] Error 1 Aug 11 03:25:38.172 INFO kablam! thread 'main' panicked at 'failed to build htslib', build.rs:59:9 Aug 11 03:25:38.172 INFO kablam! stack backtrace: Aug 11 03:25:38.172 INFO kablam! 0: 0x56294646d37e - std::sys::unix::backtrace::tracing::imp::unwind_backtrace::h72fea86a8d8797cb Aug 11 03:25:38.172 INFO kablam! at libstd/sys/unix/backtrace/tracing/gcc_s.rs:49 Aug 11 03:25:38.172 INFO kablam! 1: 0x562946461436 - std::sys_common::backtrace::print::h18c103247e00293e Aug 11 03:25:38.172 INFO kablam! at libstd/sys_common/backtrace.rs:71 Aug 11 03:25:38.172 INFO kablam! at libstd/sys_common/backtrace.rs:59 Aug 11 03:25:38.172 INFO kablam! 2: 0x56294645d19d - std::panicking::default_hook::{{closure}}::h3ad4677b789cfc8f Aug 11 03:25:38.173 INFO kablam! at libstd/panicking.rs:211 Aug 11 03:25:38.173 INFO kablam! 3: 0x56294645cf10 - std::panicking::default_hook::h051a84cdda22d0e9 Aug 11 03:25:38.173 INFO kablam! at libstd/panicking.rs:227 Aug 11 03:25:38.173 INFO kablam! 4: 0x56294645d80c - std::panicking::rust_panic_with_hook::h3c6af9682333009d Aug 11 03:25:38.173 INFO kablam! at libstd/panicking.rs:475 Aug 11 03:25:38.173 INFO kablam! 5: 0x56294629b40f - std::panicking::begin_panic::h2727c965f6a9f52f Aug 11 03:25:38.173 INFO kablam! at /checkout/src/libstd/panicking.rs:409 Aug 11 03:25:38.173 INFO kablam! 6: 0x562945e91788 - build_script_build::main::h00a092892fbdc4b3 Aug 11 03:25:38.173 INFO kablam! at /source/build.rs:59 Aug 11 03:25:38.173 INFO kablam! 7: 0x562945e9274f - std::rt::lang_start::{{closure}}::ha17dc4cb8766a5e6 Aug 11 03:25:38.173 INFO kablam! at /checkout/src/libstd/rt.rs:74 Aug 11 03:25:38.173 INFO kablam! 8: 0x56294645d2a2 - std::panicking::try::do_call::h713e323c3e2f245d Aug 11 03:25:38.173 INFO kablam! at libstd/rt.rs:59 Aug 11 03:25:38.173 INFO kablam! at libstd/panicking.rs:310 Aug 11 03:25:38.173 INFO kablam! 9: 0x56294647feb9 - __rust_maybe_catch_panic Aug 11 03:25:38.173 INFO kablam! at libpanic_unwind/lib.rs:105 Aug 11 03:25:38.173 INFO kablam! 10: 0x5629464672e5 - std::rt::lang_start_internal::hc2204b482a71dd4a Aug 11 03:25:38.173 INFO kablam! at libstd/panicking.rs:289 Aug 11 03:25:38.173 INFO kablam! at libstd/panic.rs:392 Aug 11 03:25:38.173 INFO kablam! at libstd/rt.rs:58 Aug 11 03:25:38.173 INFO kablam! 11: 0x562945e92727 - std::rt::lang_start::h155cbf1d1575b107 Aug 11 03:25:38.173 INFO kablam! at /checkout/src/libstd/rt.rs:74 Aug 11 03:25:38.173 INFO kablam! 12: 0x562945e91c59 - main Aug 11 03:25:38.173 INFO kablam! 13: 0x7f6f0f08782f - __libc_start_main Aug 11 03:25:38.173 INFO kablam! 14: 0x562945e90e08 - _start Aug 11 03:25:38.173 INFO kablam! 15: 0x0 - Aug 11 03:25:38.173 INFO kablam! Aug 11 03:25:38.177 INFO kablam! su: No module specific data is present Aug 11 03:25:38.805 INFO running `"docker" "rm" "-f" "0df56f42cc77d8e2a9df69e6594d00a4d12452393f0f556f5ccfb4e9e589d93d"` Aug 11 03:25:38.993 INFO blam! 0df56f42cc77d8e2a9df69e6594d00a4d12452393f0f556f5ccfb4e9e589d93d