Sep 01 08:13:58.238 INFO checking rust-htslib-0.21.0 against master#1114ab684fbad001c4e580326d8eb4d8c4e917d3 for pr-53831 Sep 01 08:13:58.238 INFO running: cargo +1114ab684fbad001c4e580326d8eb4d8c4e917d3-alt check --frozen --all --all-targets Sep 01 08:13:58.238 INFO running `"docker" "create" "-v" "/home/ec2-user/crater/./work/local/test-source/worker-1/pr-53831/master#1114ab684fbad001c4e580326d8eb4d8c4e917d3:/source:ro,Z" "-v" "/home/ec2-user/crater/./work/local/target-dirs/pr-53831/worker-1/master#1114ab684fbad001c4e580326d8eb4d8c4e917d3:/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 +1114ab684fbad001c4e580326d8eb4d8c4e917d3-alt check --frozen --all --all-targets" "-e" "CARGO_INCREMENTAL=0" "-e" "RUST_BACKTRACE=full" "-e" "RUSTFLAGS=--cap-lints=forbid" "-m" "2G" "crater"` Sep 01 08:13:58.503 INFO blam! b3758071f4f6689bb203ba045055abbb20873715eabe3ec3f25d83ff5007ea59 Sep 01 08:13:58.505 INFO running `"docker" "start" "-a" "b3758071f4f6689bb203ba045055abbb20873715eabe3ec3f25d83ff5007ea59"` Sep 01 08:13:59.569 INFO kablam! Checking linear-map v1.2.0 Sep 01 08:13:59.573 INFO kablam! Compiling fs-utils v1.1.0 Sep 01 08:13:59.575 INFO kablam! Checking bio-types v0.2.0 Sep 01 08:14:01.304 INFO kablam! Compiling rust-htslib v0.21.0 (file:///source) Sep 01 08:14:25.435 INFO kablam! error: failed to run custom build command for `rust-htslib v0.21.0 (file:///source)` Sep 01 08:14:25.435 INFO kablam! process didn't exit successfully: `/target/debug/build/rust-htslib-b8183217a0b95ba1/build-script-build` (exit code: 101) Sep 01 08:14:25.435 INFO kablam! --- stdout Sep 01 08:14:25.435 INFO kablam! echo '/* Default config.h generated by Makefile */' > config.h Sep 01 08:14:25.435 INFO kablam! echo '#define HAVE_LIBBZ2 1' >> config.h Sep 01 08:14:25.435 INFO kablam! echo '#define HAVE_LIBLZMA 1' >> config.h Sep 01 08:14:25.435 INFO kablam! echo '#define HAVE_FSEEKO 1' >> config.h Sep 01 08:14:25.435 INFO kablam! echo '#define HAVE_DRAND48 1' >> config.h Sep 01 08:14:25.435 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o kfunc.o kfunc.c Sep 01 08:14:25.435 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o knetfile.o knetfile.c Sep 01 08:14:25.435 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o kstring.o kstring.c Sep 01 08:14:25.435 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o bcf_sr_sort.o bcf_sr_sort.c Sep 01 08:14:25.436 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o bgzf.o bgzf.c Sep 01 08:14:25.436 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o errmod.o errmod.c Sep 01 08:14:25.436 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o faidx.o faidx.c Sep 01 08:14:25.436 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o hfile.o hfile.c Sep 01 08:14:25.436 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o hfile_net.o hfile_net.c Sep 01 08:14:25.436 INFO kablam! echo '#define HTS_VERSION "1.6"' > version.h Sep 01 08:14:25.436 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o hts.o hts.c Sep 01 08:14:25.436 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o hts_os.o hts_os.c Sep 01 08:14:25.436 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o md5.o md5.c Sep 01 08:14:25.436 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o multipart.o multipart.c Sep 01 08:14:25.436 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o probaln.o probaln.c Sep 01 08:14:25.436 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o realn.o realn.c Sep 01 08:14:25.436 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o regidx.o regidx.c Sep 01 08:14:25.436 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o sam.o sam.c Sep 01 08:14:25.436 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o synced_bcf_reader.o synced_bcf_reader.c Sep 01 08:14:25.436 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o vcf_sweep.o vcf_sweep.c Sep 01 08:14:25.436 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o tbx.o tbx.c Sep 01 08:14:25.436 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o textutils.o textutils.c Sep 01 08:14:25.436 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o thread_pool.o thread_pool.c Sep 01 08:14:25.436 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o vcf.o vcf.c Sep 01 08:14:25.436 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o vcfutils.o vcfutils.c Sep 01 08:14:25.436 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o cram/cram_codecs.o cram/cram_codecs.c Sep 01 08:14:25.436 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o cram/cram_decode.o cram/cram_decode.c Sep 01 08:14:25.437 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o cram/cram_encode.o cram/cram_encode.c Sep 01 08:14:25.437 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o cram/cram_external.o cram/cram_external.c Sep 01 08:14:25.437 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o cram/cram_index.o cram/cram_index.c Sep 01 08:14:25.437 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o cram/cram_io.o cram/cram_io.c Sep 01 08:14:25.437 INFO kablam! Makefile:120: recipe for target 'cram/cram_io.o' failed Sep 01 08:14:25.437 INFO kablam! Sep 01 08:14:25.437 INFO kablam! --- stderr Sep 01 08:14:25.437 INFO kablam! cram/cram_io.c:57:19: fatal error: bzlib.h: No such file or directory Sep 01 08:14:25.437 INFO kablam! compilation terminated. Sep 01 08:14:25.437 INFO kablam! make: *** [cram/cram_io.o] Error 1 Sep 01 08:14:25.437 INFO kablam! thread 'main' panicked at 'failed to build htslib', build.rs:59:9 Sep 01 08:14:25.437 INFO kablam! stack backtrace: Sep 01 08:14:25.437 INFO kablam! 0: 0x562a4b1381de - std::sys::unix::backtrace::tracing::imp::unwind_backtrace::ha200f2cd684ebd49 Sep 01 08:14:25.437 INFO kablam! at libstd/sys/unix/backtrace/tracing/gcc_s.rs:49 Sep 01 08:14:25.437 INFO kablam! 1: 0x562a4b127356 - std::sys_common::backtrace::print::hfe3d4e47b4c8e48c Sep 01 08:14:25.437 INFO kablam! at libstd/sys_common/backtrace.rs:71 Sep 01 08:14:25.437 INFO kablam! at libstd/sys_common/backtrace.rs:59 Sep 01 08:14:25.437 INFO kablam! 2: 0x562a4b12568d - std::panicking::default_hook::{{closure}}::hf56af31102a42941 Sep 01 08:14:25.437 INFO kablam! at libstd/panicking.rs:211 Sep 01 08:14:25.437 INFO kablam! 3: 0x562a4b125400 - std::panicking::default_hook::ha51b5d4eb7ec526d Sep 01 08:14:25.437 INFO kablam! at libstd/panicking.rs:227 Sep 01 08:14:25.438 INFO kablam! 4: 0x562a4b125cfc - std::panicking::rust_panic_with_hook::hd585483f9daec810 Sep 01 08:14:25.438 INFO kablam! at libstd/panicking.rs:477 Sep 01 08:14:25.438 INFO kablam! 5: 0x562a4af6078f - std::panicking::begin_panic::h55df5ff229a7ae44 Sep 01 08:14:25.438 INFO kablam! at /checkout/src/libstd/panicking.rs:411 Sep 01 08:14:25.438 INFO kablam! 6: 0x562a4ab49458 - build_script_build::main::he945bb64dd2a507e Sep 01 08:14:25.438 INFO kablam! at /source/build.rs:59 Sep 01 08:14:25.438 INFO kablam! 7: 0x562a4ab4a58f - std::rt::lang_start::{{closure}}::h77235f21fa724bea Sep 01 08:14:25.438 INFO kablam! at /checkout/src/libstd/rt.rs:74 Sep 01 08:14:25.438 INFO kablam! 8: 0x562a4b125792 - std::panicking::try::do_call::hea63f5620482e896 Sep 01 08:14:25.438 INFO kablam! at libstd/rt.rs:59 Sep 01 08:14:25.438 INFO kablam! at libstd/panicking.rs:310 Sep 01 08:14:25.438 INFO kablam! 9: 0x562a4b14a0a9 - __rust_maybe_catch_panic Sep 01 08:14:25.438 INFO kablam! at libpanic_unwind/lib.rs:103 Sep 01 08:14:25.438 INFO kablam! 10: 0x562a4b132b45 - std::rt::lang_start_internal::hfd6e69240f0360f8 Sep 01 08:14:25.438 INFO kablam! at libstd/panicking.rs:289 Sep 01 08:14:25.438 INFO kablam! at libstd/panic.rs:392 Sep 01 08:14:25.438 INFO kablam! at libstd/rt.rs:58 Sep 01 08:14:25.438 INFO kablam! 11: 0x562a4ab4a567 - std::rt::lang_start::haaf2b92840e1b597 Sep 01 08:14:25.438 INFO kablam! at /checkout/src/libstd/rt.rs:74 Sep 01 08:14:25.438 INFO kablam! 12: 0x562a4ab49929 - main Sep 01 08:14:25.438 INFO kablam! 13: 0x7f3cf0b2882f - __libc_start_main Sep 01 08:14:25.439 INFO kablam! 14: 0x562a4ab48ad8 - _start Sep 01 08:14:25.439 INFO kablam! 15: 0x0 - Sep 01 08:14:25.439 INFO kablam! Sep 01 08:14:25.439 INFO kablam! su: No module specific data is present Sep 01 08:14:25.839 INFO running `"docker" "rm" "-f" "b3758071f4f6689bb203ba045055abbb20873715eabe3ec3f25d83ff5007ea59"` Sep 01 08:14:25.942 INFO blam! b3758071f4f6689bb203ba045055abbb20873715eabe3ec3f25d83ff5007ea59