Sep 14 10:02:26.571 INFO checking rust-htslib-0.21.0 against master#90d36fb5905bbe5004f5b465ea14b53d10dae260 for pr-53578-1 Sep 14 10:02:26.571 INFO running: cargo +90d36fb5905bbe5004f5b465ea14b53d10dae260-alt check --frozen --all --all-targets Sep 14 10:02:26.571 INFO running `"docker" "create" "-v" "/home/ec2-user/crater/./work/local/test-source/worker-4/pr-53578-1/master#90d36fb5905bbe5004f5b465ea14b53d10dae260:/source:ro,Z" "-v" "/home/ec2-user/crater/./work/local/target-dirs/pr-53578-1/worker-4/master#90d36fb5905bbe5004f5b465ea14b53d10dae260:/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 +90d36fb5905bbe5004f5b465ea14b53d10dae260-alt check --frozen --all --all-targets" "-e" "CARGO_INCREMENTAL=0" "-e" "RUST_BACKTRACE=full" "-e" "RUSTFLAGS=--cap-lints=forbid" "-m" "2G" "crater"` Sep 14 10:02:27.105 INFO blam! f3d47c1eaffc2fbd7e860cf8f9c9d07d43edea468ba4fa1be4a6b2e16d6d6834 Sep 14 10:02:27.107 INFO running `"docker" "start" "-a" "f3d47c1eaffc2fbd7e860cf8f9c9d07d43edea468ba4fa1be4a6b2e16d6d6834"` Sep 14 10:02:28.635 INFO kablam! usermod: no changes Sep 14 10:02:28.946 INFO kablam! Compiling bindgen v0.36.1 Sep 14 10:02:28.947 INFO kablam! Checking ieee754 v0.2.2 Sep 14 10:02:28.947 INFO kablam! Checking custom_derive v0.1.7 Sep 14 10:02:28.947 INFO kablam! Checking linear-map v1.2.0 Sep 14 10:02:28.947 INFO kablam! Compiling clang-sys v0.22.0 Sep 14 10:02:28.947 INFO kablam! Compiling fs-utils v1.1.0 Sep 14 10:02:28.954 INFO kablam! Compiling newtype_derive v0.1.6 Sep 14 10:02:28.954 INFO kablam! Checking bio-types v0.2.0 Sep 14 10:02:58.000 INFO kablam! Compiling rust-htslib v0.21.0 (file:///source) Sep 14 10:03:20.030 INFO kablam! error: failed to run custom build command for `rust-htslib v0.21.0 (file:///source)` Sep 14 10:03:20.031 INFO kablam! process didn't exit successfully: `/target/debug/build/rust-htslib-3fd43cd09180d7ea/build-script-build` (exit code: 101) Sep 14 10:03:20.031 INFO kablam! --- stdout Sep 14 10:03:20.031 INFO kablam! echo '/* Default config.h generated by Makefile */' > config.h Sep 14 10:03:20.031 INFO kablam! echo '#define HAVE_LIBBZ2 1' >> config.h Sep 14 10:03:20.031 INFO kablam! echo '#define HAVE_LIBLZMA 1' >> config.h Sep 14 10:03:20.031 INFO kablam! echo '#define HAVE_FSEEKO 1' >> config.h Sep 14 10:03:20.031 INFO kablam! echo '#define HAVE_DRAND48 1' >> config.h Sep 14 10:03:20.031 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o kfunc.o kfunc.c Sep 14 10:03:20.031 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o knetfile.o knetfile.c Sep 14 10:03:20.031 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o kstring.o kstring.c Sep 14 10:03:20.031 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o bcf_sr_sort.o bcf_sr_sort.c Sep 14 10:03:20.031 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o bgzf.o bgzf.c Sep 14 10:03:20.031 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o errmod.o errmod.c Sep 14 10:03:20.031 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o faidx.o faidx.c Sep 14 10:03:20.031 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o hfile.o hfile.c Sep 14 10:03:20.031 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o hfile_net.o hfile_net.c Sep 14 10:03:20.031 INFO kablam! echo '#define HTS_VERSION "1.6"' > version.h Sep 14 10:03:20.031 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o hts.o hts.c Sep 14 10:03:20.031 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o hts_os.o hts_os.c Sep 14 10:03:20.031 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o md5.o md5.c Sep 14 10:03:20.031 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o multipart.o multipart.c Sep 14 10:03:20.031 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o probaln.o probaln.c Sep 14 10:03:20.031 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o realn.o realn.c Sep 14 10:03:20.031 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o regidx.o regidx.c Sep 14 10:03:20.031 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o sam.o sam.c Sep 14 10:03:20.031 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o synced_bcf_reader.o synced_bcf_reader.c Sep 14 10:03:20.031 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o vcf_sweep.o vcf_sweep.c Sep 14 10:03:20.031 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o tbx.o tbx.c Sep 14 10:03:20.031 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o textutils.o textutils.c Sep 14 10:03:20.031 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o thread_pool.o thread_pool.c Sep 14 10:03:20.031 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o vcf.o vcf.c Sep 14 10:03:20.031 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o vcfutils.o vcfutils.c Sep 14 10:03:20.031 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o cram/cram_codecs.o cram/cram_codecs.c Sep 14 10:03:20.031 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o cram/cram_decode.o cram/cram_decode.c Sep 14 10:03:20.031 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o cram/cram_encode.o cram/cram_encode.c Sep 14 10:03:20.031 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o cram/cram_external.o cram/cram_external.c Sep 14 10:03:20.031 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o cram/cram_index.o cram/cram_index.c Sep 14 10:03:20.031 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o cram/cram_io.o cram/cram_io.c Sep 14 10:03:20.031 INFO kablam! Makefile:120: recipe for target 'cram/cram_io.o' failed Sep 14 10:03:20.031 INFO kablam! Sep 14 10:03:20.031 INFO kablam! --- stderr Sep 14 10:03:20.031 INFO kablam! cram/cram_io.c:57:19: fatal error: bzlib.h: No such file or directory Sep 14 10:03:20.031 INFO kablam! compilation terminated. Sep 14 10:03:20.031 INFO kablam! make: *** [cram/cram_io.o] Error 1 Sep 14 10:03:20.031 INFO kablam! thread 'main' panicked at 'failed to build htslib', build.rs:59:9 Sep 14 10:03:20.031 INFO kablam! stack backtrace: Sep 14 10:03:20.031 INFO kablam! 0: 0x55f9841e302e - std::sys::unix::backtrace::tracing::imp::unwind_backtrace::hf74b7486aef10c8d Sep 14 10:03:20.031 INFO kablam! at libstd/sys/unix/backtrace/tracing/gcc_s.rs:49 Sep 14 10:03:20.031 INFO kablam! 1: 0x55f9841d2106 - std::sys_common::backtrace::print::h975e2d3548a0dd13 Sep 14 10:03:20.031 INFO kablam! at libstd/sys_common/backtrace.rs:71 Sep 14 10:03:20.031 INFO kablam! at libstd/sys_common/backtrace.rs:59 Sep 14 10:03:20.031 INFO kablam! 2: 0x55f9841d04dd - std::panicking::default_hook::{{closure}}::h3e9ae6698e7d3880 Sep 14 10:03:20.031 INFO kablam! at libstd/panicking.rs:211 Sep 14 10:03:20.031 INFO kablam! 3: 0x55f9841d0250 - std::panicking::default_hook::h0f94f2ff4ea79253 Sep 14 10:03:20.031 INFO kablam! at libstd/panicking.rs:227 Sep 14 10:03:20.031 INFO kablam! 4: 0x55f9841d0b4c - std::panicking::rust_panic_with_hook::h3122ef85eb8796fa Sep 14 10:03:20.031 INFO kablam! at libstd/panicking.rs:477 Sep 14 10:03:20.031 INFO kablam! 5: 0x55f9841379bf - std::panicking::begin_panic::h292d643e76baa677 Sep 14 10:03:20.031 INFO kablam! at /checkout/src/libstd/panicking.rs:411 Sep 14 10:03:20.031 INFO kablam! 6: 0x55f983bf7394 - build_script_build::main::h87235bb048d04118 Sep 14 10:03:20.031 INFO kablam! at /source/build.rs:59 Sep 14 10:03:20.031 INFO kablam! 7: 0x55f983bf84bf - std::rt::lang_start::{{closure}}::h7c03edd05515c394 Sep 14 10:03:20.031 INFO kablam! at /checkout/src/libstd/rt.rs:74 Sep 14 10:03:20.031 INFO kablam! 8: 0x55f9841d05e2 - std::panicking::try::do_call::h613cc8345e5e334f Sep 14 10:03:20.031 INFO kablam! at libstd/rt.rs:59 Sep 14 10:03:20.031 INFO kablam! at libstd/panicking.rs:310 Sep 14 10:03:20.031 INFO kablam! 9: 0x55f9841f5d19 - __rust_maybe_catch_panic Sep 14 10:03:20.031 INFO kablam! at libpanic_unwind/lib.rs:102 Sep 14 10:03:20.031 INFO kablam! 10: 0x55f9841dda15 - std::rt::lang_start_internal::h166c3316158aaef7 Sep 14 10:03:20.031 INFO kablam! at libstd/panicking.rs:289 Sep 14 10:03:20.031 INFO kablam! at libstd/panic.rs:392 Sep 14 10:03:20.031 INFO kablam! at libstd/rt.rs:58 Sep 14 10:03:20.032 INFO kablam! 11: 0x55f983bf8497 - std::rt::lang_start::h411dbb54c043ba5f Sep 14 10:03:20.032 INFO kablam! at /checkout/src/libstd/rt.rs:74 Sep 14 10:03:20.032 INFO kablam! 12: 0x55f983bf7859 - main Sep 14 10:03:20.032 INFO kablam! 13: 0x7fc13357682f - __libc_start_main Sep 14 10:03:20.032 INFO kablam! 14: 0x55f983bf6a48 - _start Sep 14 10:03:20.032 INFO kablam! 15: 0x0 - Sep 14 10:03:20.032 INFO kablam! Sep 14 10:03:20.032 INFO kablam! su: No module specific data is present Sep 14 10:03:20.584 INFO running `"docker" "rm" "-f" "f3d47c1eaffc2fbd7e860cf8f9c9d07d43edea468ba4fa1be4a6b2e16d6d6834"` Sep 14 10:03:20.686 INFO blam! f3d47c1eaffc2fbd7e860cf8f9c9d07d43edea468ba4fa1be4a6b2e16d6d6834