Sep 02 01:33:50.026 INFO checking rust-htslib-0.21.0 against master#1114ab684fbad001c4e580326d8eb4d8c4e917d3 for pr-53851 Sep 02 01:33:50.026 INFO running: cargo +1114ab684fbad001c4e580326d8eb4d8c4e917d3-alt check --frozen --all --all-targets Sep 02 01:33:50.026 INFO running `"docker" "create" "-v" "/home/ec2-user/crater/./work/local/test-source/worker-0/pr-53851/master#1114ab684fbad001c4e580326d8eb4d8c4e917d3:/source:ro,Z" "-v" "/home/ec2-user/crater/./work/local/target-dirs/pr-53851/worker-0/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 02 01:33:50.289 INFO blam! cb991644eaf39ce38509c9d958eed59ce61f70cc7f7b8d61b68c4d418afa5ef5 Sep 02 01:33:50.292 INFO running `"docker" "start" "-a" "cb991644eaf39ce38509c9d958eed59ce61f70cc7f7b8d61b68c4d418afa5ef5"` Sep 02 01:33:51.374 INFO kablam! Checking linear-map v1.2.0 Sep 02 01:33:51.398 INFO kablam! Compiling fs-utils v1.1.0 Sep 02 01:33:51.425 INFO kablam! Checking bio-types v0.2.0 Sep 02 01:33:52.972 INFO kablam! Compiling rust-htslib v0.21.0 (file:///source) Sep 02 01:34:15.941 INFO kablam! error: failed to run custom build command for `rust-htslib v0.21.0 (file:///source)` Sep 02 01:34:15.941 INFO kablam! process didn't exit successfully: `/target/debug/build/rust-htslib-b8183217a0b95ba1/build-script-build` (exit code: 101) Sep 02 01:34:15.941 INFO kablam! --- stdout Sep 02 01:34:15.941 INFO kablam! echo '/* Default config.h generated by Makefile */' > config.h Sep 02 01:34:15.941 INFO kablam! echo '#define HAVE_LIBBZ2 1' >> config.h Sep 02 01:34:15.941 INFO kablam! echo '#define HAVE_LIBLZMA 1' >> config.h Sep 02 01:34:15.941 INFO kablam! echo '#define HAVE_FSEEKO 1' >> config.h Sep 02 01:34:15.941 INFO kablam! echo '#define HAVE_DRAND48 1' >> config.h Sep 02 01:34:15.941 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o kfunc.o kfunc.c Sep 02 01:34:15.941 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o knetfile.o knetfile.c Sep 02 01:34:15.941 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o kstring.o kstring.c Sep 02 01:34:15.941 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o bcf_sr_sort.o bcf_sr_sort.c Sep 02 01:34:15.942 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o bgzf.o bgzf.c Sep 02 01:34:15.942 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o errmod.o errmod.c Sep 02 01:34:15.942 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o faidx.o faidx.c Sep 02 01:34:15.942 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o hfile.o hfile.c Sep 02 01:34:15.942 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o hfile_net.o hfile_net.c Sep 02 01:34:15.942 INFO kablam! echo '#define HTS_VERSION "1.6"' > version.h Sep 02 01:34:15.942 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o hts.o hts.c Sep 02 01:34:15.942 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o hts_os.o hts_os.c Sep 02 01:34:15.942 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o md5.o md5.c Sep 02 01:34:15.942 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o multipart.o multipart.c Sep 02 01:34:15.942 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o probaln.o probaln.c Sep 02 01:34:15.942 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o realn.o realn.c Sep 02 01:34:15.942 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o regidx.o regidx.c Sep 02 01:34:15.942 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o sam.o sam.c Sep 02 01:34:15.942 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o synced_bcf_reader.o synced_bcf_reader.c Sep 02 01:34:15.942 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o vcf_sweep.o vcf_sweep.c Sep 02 01:34:15.942 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o tbx.o tbx.c Sep 02 01:34:15.943 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o textutils.o textutils.c Sep 02 01:34:15.943 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o thread_pool.o thread_pool.c Sep 02 01:34:15.943 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o vcf.o vcf.c Sep 02 01:34:15.943 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o vcfutils.o vcfutils.c Sep 02 01:34:15.943 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o cram/cram_codecs.o cram/cram_codecs.c Sep 02 01:34:15.943 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o cram/cram_decode.o cram/cram_decode.c Sep 02 01:34:15.943 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o cram/cram_encode.o cram/cram_encode.c Sep 02 01:34:15.943 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o cram/cram_external.o cram/cram_external.c Sep 02 01:34:15.943 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o cram/cram_index.o cram/cram_index.c Sep 02 01:34:15.943 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o cram/cram_io.o cram/cram_io.c Sep 02 01:34:15.943 INFO kablam! Makefile:120: recipe for target 'cram/cram_io.o' failed Sep 02 01:34:15.943 INFO kablam! Sep 02 01:34:15.943 INFO kablam! --- stderr Sep 02 01:34:15.943 INFO kablam! cram/cram_io.c:57:19: fatal error: bzlib.h: No such file or directory Sep 02 01:34:15.943 INFO kablam! compilation terminated. Sep 02 01:34:15.943 INFO kablam! make: *** [cram/cram_io.o] Error 1 Sep 02 01:34:15.943 INFO kablam! thread 'main' panicked at 'failed to build htslib', build.rs:59:9 Sep 02 01:34:15.944 INFO kablam! stack backtrace: Sep 02 01:34:15.944 INFO kablam! 0: 0x56066bbb51de - std::sys::unix::backtrace::tracing::imp::unwind_backtrace::ha200f2cd684ebd49 Sep 02 01:34:15.944 INFO kablam! at libstd/sys/unix/backtrace/tracing/gcc_s.rs:49 Sep 02 01:34:15.944 INFO kablam! 1: 0x56066bba4356 - std::sys_common::backtrace::print::hfe3d4e47b4c8e48c Sep 02 01:34:15.944 INFO kablam! at libstd/sys_common/backtrace.rs:71 Sep 02 01:34:15.944 INFO kablam! at libstd/sys_common/backtrace.rs:59 Sep 02 01:34:15.944 INFO kablam! 2: 0x56066bba268d - std::panicking::default_hook::{{closure}}::hf56af31102a42941 Sep 02 01:34:15.944 INFO kablam! at libstd/panicking.rs:211 Sep 02 01:34:15.944 INFO kablam! 3: 0x56066bba2400 - std::panicking::default_hook::ha51b5d4eb7ec526d Sep 02 01:34:15.944 INFO kablam! at libstd/panicking.rs:227 Sep 02 01:34:15.944 INFO kablam! 4: 0x56066bba2cfc - std::panicking::rust_panic_with_hook::hd585483f9daec810 Sep 02 01:34:15.944 INFO kablam! at libstd/panicking.rs:477 Sep 02 01:34:15.944 INFO kablam! 5: 0x56066b9dd78f - std::panicking::begin_panic::h55df5ff229a7ae44 Sep 02 01:34:15.944 INFO kablam! at /checkout/src/libstd/panicking.rs:411 Sep 02 01:34:15.944 INFO kablam! 6: 0x56066b5c6458 - build_script_build::main::he945bb64dd2a507e Sep 02 01:34:15.944 INFO kablam! at /source/build.rs:59 Sep 02 01:34:15.944 INFO kablam! 7: 0x56066b5c758f - std::rt::lang_start::{{closure}}::h77235f21fa724bea Sep 02 01:34:15.944 INFO kablam! at /checkout/src/libstd/rt.rs:74 Sep 02 01:34:15.945 INFO kablam! 8: 0x56066bba2792 - std::panicking::try::do_call::hea63f5620482e896 Sep 02 01:34:15.945 INFO kablam! at libstd/rt.rs:59 Sep 02 01:34:15.945 INFO kablam! at libstd/panicking.rs:310 Sep 02 01:34:15.945 INFO kablam! 9: 0x56066bbc70a9 - __rust_maybe_catch_panic Sep 02 01:34:15.945 INFO kablam! at libpanic_unwind/lib.rs:103 Sep 02 01:34:15.945 INFO kablam! 10: 0x56066bbafb45 - std::rt::lang_start_internal::hfd6e69240f0360f8 Sep 02 01:34:15.945 INFO kablam! at libstd/panicking.rs:289 Sep 02 01:34:15.945 INFO kablam! at libstd/panic.rs:392 Sep 02 01:34:15.945 INFO kablam! at libstd/rt.rs:58 Sep 02 01:34:15.945 INFO kablam! 11: 0x56066b5c7567 - std::rt::lang_start::haaf2b92840e1b597 Sep 02 01:34:15.945 INFO kablam! at /checkout/src/libstd/rt.rs:74 Sep 02 01:34:15.945 INFO kablam! 12: 0x56066b5c6929 - main Sep 02 01:34:15.945 INFO kablam! 13: 0x7f688953582f - __libc_start_main Sep 02 01:34:15.945 INFO kablam! 14: 0x56066b5c5ad8 - _start Sep 02 01:34:15.945 INFO kablam! 15: 0x0 - Sep 02 01:34:15.945 INFO kablam! Sep 02 01:34:15.945 INFO kablam! su: No module specific data is present Sep 02 01:34:16.431 INFO running `"docker" "rm" "-f" "cb991644eaf39ce38509c9d958eed59ce61f70cc7f7b8d61b68c4d418afa5ef5"` Sep 02 01:34:16.514 INFO blam! cb991644eaf39ce38509c9d958eed59ce61f70cc7f7b8d61b68c4d418afa5ef5