Aug 30 05:10:04.568 INFO checking rust-htslib-0.21.0 against master#ede55518431154bc761f7b2438cce9078c162700 for pr-53707 Aug 30 05:10:04.569 INFO running: cargo +ede55518431154bc761f7b2438cce9078c162700-alt check --frozen --all --all-targets Aug 30 05:10:04.569 INFO running `"docker" "create" "-v" "/home/ec2-user/crater/./work/local/test-source/worker-1/pr-53707/master#ede55518431154bc761f7b2438cce9078c162700:/source:ro,Z" "-v" "/home/ec2-user/crater/./work/local/target-dirs/pr-53707/worker-1/master#ede55518431154bc761f7b2438cce9078c162700:/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=500" "-e" "CMD=cargo +ede55518431154bc761f7b2438cce9078c162700-alt check --frozen --all --all-targets" "-e" "CARGO_INCREMENTAL=0" "-e" "RUST_BACKTRACE=full" "-e" "RUSTFLAGS=--cap-lints=forbid" "-m" "2G" "crater"` Aug 30 05:10:04.794 INFO blam! ca98780e48cd36f0a63b50424cfef3dd187a868c1a60f288e9183e2e67e82b73 Aug 30 05:10:04.794 INFO running `"docker" "start" "-a" "ca98780e48cd36f0a63b50424cfef3dd187a868c1a60f288e9183e2e67e82b73"` Aug 30 05:10:05.853 INFO kablam! Checking linear-map v1.2.0 Aug 30 05:10:05.853 INFO kablam! Checking ieee754 v0.2.2 Aug 30 05:10:05.855 INFO kablam! Compiling fs-utils v1.1.0 Aug 30 05:10:05.857 INFO kablam! Checking bio-types v0.2.0 Aug 30 05:10:08.009 INFO kablam! Compiling rust-htslib v0.21.0 (file:///source) Aug 30 05:10:30.262 INFO kablam! error: failed to run custom build command for `rust-htslib v0.21.0 (file:///source)` Aug 30 05:10:30.262 INFO kablam! process didn't exit successfully: `/target/debug/build/rust-htslib-ef3379d507cce5ea/build-script-build` (exit code: 101) Aug 30 05:10:30.262 INFO kablam! --- stdout Aug 30 05:10:30.262 INFO kablam! echo '/* Default config.h generated by Makefile */' > config.h Aug 30 05:10:30.262 INFO kablam! echo '#define HAVE_LIBBZ2 1' >> config.h Aug 30 05:10:30.262 INFO kablam! echo '#define HAVE_LIBLZMA 1' >> config.h Aug 30 05:10:30.262 INFO kablam! echo '#define HAVE_FSEEKO 1' >> config.h Aug 30 05:10:30.262 INFO kablam! echo '#define HAVE_DRAND48 1' >> config.h Aug 30 05:10:30.262 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o kfunc.o kfunc.c Aug 30 05:10:30.262 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o knetfile.o knetfile.c Aug 30 05:10:30.262 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o kstring.o kstring.c Aug 30 05:10:30.262 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o bcf_sr_sort.o bcf_sr_sort.c Aug 30 05:10:30.262 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o bgzf.o bgzf.c Aug 30 05:10:30.262 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o errmod.o errmod.c Aug 30 05:10:30.262 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o faidx.o faidx.c Aug 30 05:10:30.263 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o hfile.o hfile.c Aug 30 05:10:30.263 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o hfile_net.o hfile_net.c Aug 30 05:10:30.263 INFO kablam! echo '#define HTS_VERSION "1.6"' > version.h Aug 30 05:10:30.263 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o hts.o hts.c Aug 30 05:10:30.263 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o hts_os.o hts_os.c Aug 30 05:10:30.263 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o md5.o md5.c Aug 30 05:10:30.263 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o multipart.o multipart.c Aug 30 05:10:30.263 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o probaln.o probaln.c Aug 30 05:10:30.263 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o realn.o realn.c Aug 30 05:10:30.263 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o regidx.o regidx.c Aug 30 05:10:30.263 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o sam.o sam.c Aug 30 05:10:30.263 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o synced_bcf_reader.o synced_bcf_reader.c Aug 30 05:10:30.263 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o vcf_sweep.o vcf_sweep.c Aug 30 05:10:30.263 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o tbx.o tbx.c Aug 30 05:10:30.263 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o textutils.o textutils.c Aug 30 05:10:30.263 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o thread_pool.o thread_pool.c Aug 30 05:10:30.263 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o vcf.o vcf.c Aug 30 05:10:30.263 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o vcfutils.o vcfutils.c Aug 30 05:10:30.263 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o cram/cram_codecs.o cram/cram_codecs.c Aug 30 05:10:30.263 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o cram/cram_decode.o cram/cram_decode.c Aug 30 05:10:30.263 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o cram/cram_encode.o cram/cram_encode.c Aug 30 05:10:30.263 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o cram/cram_external.o cram/cram_external.c Aug 30 05:10:30.263 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o cram/cram_index.o cram/cram_index.c Aug 30 05:10:30.263 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o cram/cram_io.o cram/cram_io.c Aug 30 05:10:30.263 INFO kablam! Makefile:120: recipe for target 'cram/cram_io.o' failed Aug 30 05:10:30.263 INFO kablam! Aug 30 05:10:30.263 INFO kablam! --- stderr Aug 30 05:10:30.263 INFO kablam! cram/cram_io.c:57:19: fatal error: bzlib.h: No such file or directory Aug 30 05:10:30.263 INFO kablam! compilation terminated. Aug 30 05:10:30.264 INFO kablam! make: *** [cram/cram_io.o] Error 1 Aug 30 05:10:30.264 INFO kablam! thread 'main' panicked at 'failed to build htslib', build.rs:59:9 Aug 30 05:10:30.264 INFO kablam! stack backtrace: Aug 30 05:10:30.264 INFO kablam! 0: 0x55e0d53df21e - std::sys::unix::backtrace::tracing::imp::unwind_backtrace::h2e24c3aef5ef21db Aug 30 05:10:30.264 INFO kablam! at libstd/sys/unix/backtrace/tracing/gcc_s.rs:49 Aug 30 05:10:30.264 INFO kablam! 1: 0x55e0d53ce376 - std::sys_common::backtrace::print::hc5f2ea19f5e117e2 Aug 30 05:10:30.264 INFO kablam! at libstd/sys_common/backtrace.rs:71 Aug 30 05:10:30.264 INFO kablam! at libstd/sys_common/backtrace.rs:59 Aug 30 05:10:30.264 INFO kablam! 2: 0x55e0d53cc6ad - std::panicking::default_hook::{{closure}}::h708048e2809fc48c Aug 30 05:10:30.264 INFO kablam! at libstd/panicking.rs:211 Aug 30 05:10:30.264 INFO kablam! 3: 0x55e0d53cc420 - std::panicking::default_hook::h6b6759214d380e57 Aug 30 05:10:30.264 INFO kablam! at libstd/panicking.rs:227 Aug 30 05:10:30.264 INFO kablam! 4: 0x55e0d53ccd1c - std::panicking::rust_panic_with_hook::h1e37970c6180beb4 Aug 30 05:10:30.264 INFO kablam! at libstd/panicking.rs:477 Aug 30 05:10:30.264 INFO kablam! 5: 0x55e0d5162d0f - std::panicking::begin_panic::h37d80f3f23626ff7 Aug 30 05:10:30.264 INFO kablam! at /checkout/src/libstd/panicking.rs:411 Aug 30 05:10:30.264 INFO kablam! 6: 0x55e0d4df0458 - build_script_build::main::hb75d12b154fc0778 Aug 30 05:10:30.264 INFO kablam! at /source/build.rs:59 Aug 30 05:10:30.264 INFO kablam! 7: 0x55e0d4df158f - std::rt::lang_start::{{closure}}::h2d1eeb9947be2fd9 Aug 30 05:10:30.264 INFO kablam! at /checkout/src/libstd/rt.rs:74 Aug 30 05:10:30.264 INFO kablam! 8: 0x55e0d53cc7b2 - std::panicking::try::do_call::h34654e345c0ff9fc Aug 30 05:10:30.264 INFO kablam! at libstd/rt.rs:59 Aug 30 05:10:30.264 INFO kablam! at libstd/panicking.rs:310 Aug 30 05:10:30.264 INFO kablam! 9: 0x55e0d53f13e9 - __rust_maybe_catch_panic Aug 30 05:10:30.264 INFO kablam! at libpanic_unwind/lib.rs:102 Aug 30 05:10:30.264 INFO kablam! 10: 0x55e0d53d9b85 - std::rt::lang_start_internal::h0b4f47076f8cba18 Aug 30 05:10:30.264 INFO kablam! at libstd/panicking.rs:289 Aug 30 05:10:30.264 INFO kablam! at libstd/panic.rs:392 Aug 30 05:10:30.265 INFO kablam! at libstd/rt.rs:58 Aug 30 05:10:30.265 INFO kablam! 11: 0x55e0d4df1567 - std::rt::lang_start::h89a8ad1d8f01d46e Aug 30 05:10:30.265 INFO kablam! at /checkout/src/libstd/rt.rs:74 Aug 30 05:10:30.265 INFO kablam! 12: 0x55e0d4df0929 - main Aug 30 05:10:30.265 INFO kablam! 13: 0x7f863beb682f - __libc_start_main Aug 30 05:10:30.265 INFO kablam! 14: 0x55e0d4defad8 - _start Aug 30 05:10:30.265 INFO kablam! 15: 0x0 - Aug 30 05:10:30.265 INFO kablam! Aug 30 05:10:30.265 INFO kablam! su: No module specific data is present Aug 30 05:10:30.649 INFO running `"docker" "rm" "-f" "ca98780e48cd36f0a63b50424cfef3dd187a868c1a60f288e9183e2e67e82b73"` Aug 30 05:10:30.733 INFO blam! ca98780e48cd36f0a63b50424cfef3dd187a868c1a60f288e9183e2e67e82b73