Sep 17 18:15:49.833 INFO checking rust-htslib-0.21.0 against master#cb6d2dfa8923902b0992a1522dc4a45a9d3ba690 for pr-54033 Sep 17 18:15:49.833 INFO running: cargo +cb6d2dfa8923902b0992a1522dc4a45a9d3ba690-alt check --frozen --all --all-targets Sep 17 18:15:49.833 INFO running `"docker" "create" "-v" "/home/ec2-user/crater/./work/local/test-source/worker-1/pr-54033/master#cb6d2dfa8923902b0992a1522dc4a45a9d3ba690:/source:ro,Z" "-v" "/home/ec2-user/crater/./work/local/target-dirs/pr-54033/worker-1/master#cb6d2dfa8923902b0992a1522dc4a45a9d3ba690:/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 +cb6d2dfa8923902b0992a1522dc4a45a9d3ba690-alt check --frozen --all --all-targets" "-e" "CARGO_INCREMENTAL=0" "-e" "RUST_BACKTRACE=full" "-e" "RUSTFLAGS=--cap-lints=forbid" "-m" "1536M" "crater"` Sep 17 18:15:50.216 INFO blam! f53e3ff2de464e840c086a8f4409dc8cbfb95840aa046367465904bd1a2a674e Sep 17 18:15:50.218 INFO running `"docker" "start" "-a" "f53e3ff2de464e840c086a8f4409dc8cbfb95840aa046367465904bd1a2a674e"` Sep 17 18:15:51.217 INFO kablam! usermod: no changes Sep 17 18:15:51.566 INFO kablam! Checking ieee754 v0.2.2 Sep 17 18:15:51.567 INFO kablam! Checking custom_derive v0.1.7 Sep 17 18:15:51.567 INFO kablam! Checking linear-map v1.2.0 Sep 17 18:15:51.578 INFO kablam! Compiling fs-utils v1.1.0 Sep 17 18:15:51.579 INFO kablam! Checking bincode v1.0.1 Sep 17 18:15:51.582 INFO kablam! Checking bio-types v0.3.0 Sep 17 18:15:53.193 INFO kablam! Compiling rust-htslib v0.21.0 (/source) Sep 17 18:16:17.799 INFO kablam! error: failed to run custom build command for `rust-htslib v0.21.0 (/source)` Sep 17 18:16:17.799 INFO kablam! process didn't exit successfully: `/target/debug/build/rust-htslib-8497e0e564c220de/build-script-build` (exit code: 101) Sep 17 18:16:17.799 INFO kablam! --- stdout Sep 17 18:16:17.799 INFO kablam! echo '/* Default config.h generated by Makefile */' > config.h Sep 17 18:16:17.799 INFO kablam! echo '#define HAVE_LIBBZ2 1' >> config.h Sep 17 18:16:17.799 INFO kablam! echo '#define HAVE_LIBLZMA 1' >> config.h Sep 17 18:16:17.799 INFO kablam! echo '#define HAVE_FSEEKO 1' >> config.h Sep 17 18:16:17.799 INFO kablam! echo '#define HAVE_DRAND48 1' >> config.h Sep 17 18:16:17.799 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o kfunc.o kfunc.c Sep 17 18:16:17.799 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o knetfile.o knetfile.c Sep 17 18:16:17.799 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o kstring.o kstring.c Sep 17 18:16:17.799 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o bcf_sr_sort.o bcf_sr_sort.c Sep 17 18:16:17.799 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o bgzf.o bgzf.c Sep 17 18:16:17.799 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o errmod.o errmod.c Sep 17 18:16:17.799 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o faidx.o faidx.c Sep 17 18:16:17.799 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o hfile.o hfile.c Sep 17 18:16:17.799 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o hfile_net.o hfile_net.c Sep 17 18:16:17.799 INFO kablam! echo '#define HTS_VERSION "1.6"' > version.h Sep 17 18:16:17.799 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o hts.o hts.c Sep 17 18:16:17.799 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o hts_os.o hts_os.c Sep 17 18:16:17.799 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o md5.o md5.c Sep 17 18:16:17.799 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o multipart.o multipart.c Sep 17 18:16:17.799 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o probaln.o probaln.c Sep 17 18:16:17.799 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o realn.o realn.c Sep 17 18:16:17.799 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o regidx.o regidx.c Sep 17 18:16:17.799 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o sam.o sam.c Sep 17 18:16:17.799 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o synced_bcf_reader.o synced_bcf_reader.c Sep 17 18:16:17.799 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o vcf_sweep.o vcf_sweep.c Sep 17 18:16:17.799 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o tbx.o tbx.c Sep 17 18:16:17.799 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o textutils.o textutils.c Sep 17 18:16:17.799 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o thread_pool.o thread_pool.c Sep 17 18:16:17.800 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o vcf.o vcf.c Sep 17 18:16:17.800 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o vcfutils.o vcfutils.c Sep 17 18:16:17.800 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o cram/cram_codecs.o cram/cram_codecs.c Sep 17 18:16:17.800 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o cram/cram_decode.o cram/cram_decode.c Sep 17 18:16:17.800 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o cram/cram_encode.o cram/cram_encode.c Sep 17 18:16:17.800 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o cram/cram_external.o cram/cram_external.c Sep 17 18:16:17.800 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o cram/cram_index.o cram/cram_index.c Sep 17 18:16:17.800 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o cram/cram_io.o cram/cram_io.c Sep 17 18:16:17.800 INFO kablam! Makefile:120: recipe for target 'cram/cram_io.o' failed Sep 17 18:16:17.800 INFO kablam! Sep 17 18:16:17.800 INFO kablam! --- stderr Sep 17 18:16:17.800 INFO kablam! cram/cram_io.c:57:19: fatal error: bzlib.h: No such file or directory Sep 17 18:16:17.800 INFO kablam! compilation terminated. Sep 17 18:16:17.800 INFO kablam! make: *** [cram/cram_io.o] Error 1 Sep 17 18:16:17.800 INFO kablam! thread 'main' panicked at 'failed to build htslib', build.rs:59:9 Sep 17 18:16:17.800 INFO kablam! stack backtrace: Sep 17 18:16:17.800 INFO kablam! 0: 0x55a1f24bea7e - std::sys::unix::backtrace::tracing::imp::unwind_backtrace::he3ea2af6595cbcfd Sep 17 18:16:17.800 INFO kablam! at libstd/sys/unix/backtrace/tracing/gcc_s.rs:49 Sep 17 18:16:17.800 INFO kablam! 1: 0x55a1f24adb66 - std::sys_common::backtrace::print::h9a6dc25b0b6db3e6 Sep 17 18:16:17.800 INFO kablam! at libstd/sys_common/backtrace.rs:71 Sep 17 18:16:17.800 INFO kablam! at libstd/sys_common/backtrace.rs:59 Sep 17 18:16:17.800 INFO kablam! 2: 0x55a1f24abf3d - std::panicking::default_hook::{{closure}}::h9f9f4c00fc62ac12 Sep 17 18:16:17.800 INFO kablam! at libstd/panicking.rs:211 Sep 17 18:16:17.800 INFO kablam! 3: 0x55a1f24abcb0 - std::panicking::default_hook::h86ebe853ecef0f3c Sep 17 18:16:17.800 INFO kablam! at libstd/panicking.rs:227 Sep 17 18:16:17.800 INFO kablam! 4: 0x55a1f24ac5ac - std::panicking::rust_panic_with_hook::h6d3348b8dd4df56e Sep 17 18:16:17.800 INFO kablam! at libstd/panicking.rs:477 Sep 17 18:16:17.800 INFO kablam! 5: 0x55a1f2413fbf - std::panicking::begin_panic::h7142d6194e04df9f Sep 17 18:16:17.800 INFO kablam! at libstd/panicking.rs:411 Sep 17 18:16:17.800 INFO kablam! 6: 0x55a1f1ed3394 - build_script_build::main::ha2a90f0c2d220ce8 Sep 17 18:16:17.800 INFO kablam! at /source/build.rs:59 Sep 17 18:16:17.800 INFO kablam! 7: 0x55a1f1ed44bf - std::rt::lang_start::{{closure}}::h410c3c93a0618d72 Sep 17 18:16:17.800 INFO kablam! at libstd/rt.rs:74 Sep 17 18:16:17.800 INFO kablam! 8: 0x55a1f24ac042 - std::panicking::try::do_call::h46a7bcf1f6152e5b Sep 17 18:16:17.800 INFO kablam! at libstd/rt.rs:59 Sep 17 18:16:17.800 INFO kablam! at libstd/panicking.rs:310 Sep 17 18:16:17.800 INFO kablam! 9: 0x55a1f24d0f59 - __rust_maybe_catch_panic Sep 17 18:16:17.800 INFO kablam! at libpanic_unwind/lib.rs:102 Sep 17 18:16:17.800 INFO kablam! 10: 0x55a1f24b9465 - std::rt::lang_start_internal::h221cb5896f5e061c Sep 17 18:16:17.800 INFO kablam! at libstd/panicking.rs:289 Sep 17 18:16:17.800 INFO kablam! at libstd/panic.rs:392 Sep 17 18:16:17.800 INFO kablam! at libstd/rt.rs:58 Sep 17 18:16:17.800 INFO kablam! 11: 0x55a1f1ed4497 - std::rt::lang_start::hfef0762931c8d8f9 Sep 17 18:16:17.800 INFO kablam! at libstd/rt.rs:74 Sep 17 18:16:17.800 INFO kablam! 12: 0x55a1f1ed3859 - main Sep 17 18:16:17.800 INFO kablam! 13: 0x7fc4d4a5d82f - __libc_start_main Sep 17 18:16:17.800 INFO kablam! 14: 0x55a1f1ed2a48 - _start Sep 17 18:16:17.800 INFO kablam! 15: 0x0 - Sep 17 18:16:17.800 INFO kablam! Sep 17 18:16:17.800 INFO kablam! su: No module specific data is present Sep 17 18:16:18.355 INFO running `"docker" "rm" "-f" "f53e3ff2de464e840c086a8f4409dc8cbfb95840aa046367465904bd1a2a674e"` Sep 17 18:16:18.446 INFO blam! f53e3ff2de464e840c086a8f4409dc8cbfb95840aa046367465904bd1a2a674e