Sep 04 04:56:03.649 INFO checking rust-htslib-0.21.0 against master#28bcffead74d5e17c6cb1f7de432e37f93a6b50c for pr-53893 Sep 04 04:56:03.649 INFO running: cargo +28bcffead74d5e17c6cb1f7de432e37f93a6b50c-alt check --frozen --all --all-targets Sep 04 04:56:03.649 INFO running `"docker" "create" "-v" "/home/ec2-user/crater/./work/local/test-source/worker-0/pr-53893/master#28bcffead74d5e17c6cb1f7de432e37f93a6b50c:/source:ro,Z" "-v" "/home/ec2-user/crater/./work/local/target-dirs/pr-53893/worker-0/master#28bcffead74d5e17c6cb1f7de432e37f93a6b50c:/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 +28bcffead74d5e17c6cb1f7de432e37f93a6b50c-alt check --frozen --all --all-targets" "-e" "CARGO_INCREMENTAL=0" "-e" "RUST_BACKTRACE=full" "-e" "RUSTFLAGS=--cap-lints=forbid" "-m" "2G" "crater"` Sep 04 04:56:03.890 INFO blam! d20f51c5943e4854d9fd3bd24469513321f08a5531e5f52a4578a94d87931141 Sep 04 04:56:03.892 INFO running `"docker" "start" "-a" "d20f51c5943e4854d9fd3bd24469513321f08a5531e5f52a4578a94d87931141"` Sep 04 04:56:04.643 INFO kablam! Checking linear-map v1.2.0 Sep 04 04:56:04.644 INFO kablam! Compiling fs-utils v1.1.0 Sep 04 04:56:04.646 INFO kablam! Checking bio-types v0.2.0 Sep 04 04:56:05.796 INFO kablam! Compiling rust-htslib v0.21.0 (file:///source) Sep 04 04:56:29.676 INFO kablam! error: failed to run custom build command for `rust-htslib v0.21.0 (file:///source)` Sep 04 04:56:29.676 INFO kablam! process didn't exit successfully: `/target/debug/build/rust-htslib-99ee094251ff5849/build-script-build` (exit code: 101) Sep 04 04:56:29.676 INFO kablam! --- stdout Sep 04 04:56:29.676 INFO kablam! echo '/* Default config.h generated by Makefile */' > config.h Sep 04 04:56:29.676 INFO kablam! echo '#define HAVE_LIBBZ2 1' >> config.h Sep 04 04:56:29.676 INFO kablam! echo '#define HAVE_LIBLZMA 1' >> config.h Sep 04 04:56:29.676 INFO kablam! echo '#define HAVE_FSEEKO 1' >> config.h Sep 04 04:56:29.676 INFO kablam! echo '#define HAVE_DRAND48 1' >> config.h Sep 04 04:56:29.676 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o kfunc.o kfunc.c Sep 04 04:56:29.676 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o knetfile.o knetfile.c Sep 04 04:56:29.676 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o kstring.o kstring.c Sep 04 04:56:29.676 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o bcf_sr_sort.o bcf_sr_sort.c Sep 04 04:56:29.676 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o bgzf.o bgzf.c Sep 04 04:56:29.676 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o errmod.o errmod.c Sep 04 04:56:29.676 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o faidx.o faidx.c Sep 04 04:56:29.676 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o hfile.o hfile.c Sep 04 04:56:29.676 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o hfile_net.o hfile_net.c Sep 04 04:56:29.677 INFO kablam! echo '#define HTS_VERSION "1.6"' > version.h Sep 04 04:56:29.677 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o hts.o hts.c Sep 04 04:56:29.677 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o hts_os.o hts_os.c Sep 04 04:56:29.677 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o md5.o md5.c Sep 04 04:56:29.677 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o multipart.o multipart.c Sep 04 04:56:29.677 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o probaln.o probaln.c Sep 04 04:56:29.677 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o realn.o realn.c Sep 04 04:56:29.677 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o regidx.o regidx.c Sep 04 04:56:29.677 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o sam.o sam.c Sep 04 04:56:29.677 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o synced_bcf_reader.o synced_bcf_reader.c Sep 04 04:56:29.677 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o vcf_sweep.o vcf_sweep.c Sep 04 04:56:29.677 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o tbx.o tbx.c Sep 04 04:56:29.677 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o textutils.o textutils.c Sep 04 04:56:29.677 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o thread_pool.o thread_pool.c Sep 04 04:56:29.677 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o vcf.o vcf.c Sep 04 04:56:29.677 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o vcfutils.o vcfutils.c Sep 04 04:56:29.677 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o cram/cram_codecs.o cram/cram_codecs.c Sep 04 04:56:29.677 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o cram/cram_decode.o cram/cram_decode.c Sep 04 04:56:29.677 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o cram/cram_encode.o cram/cram_encode.c Sep 04 04:56:29.677 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o cram/cram_external.o cram/cram_external.c Sep 04 04:56:29.677 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o cram/cram_index.o cram/cram_index.c Sep 04 04:56:29.677 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o cram/cram_io.o cram/cram_io.c Sep 04 04:56:29.677 INFO kablam! Makefile:120: recipe for target 'cram/cram_io.o' failed Sep 04 04:56:29.677 INFO kablam! Sep 04 04:56:29.677 INFO kablam! --- stderr Sep 04 04:56:29.677 INFO kablam! cram/cram_io.c:57:19: fatal error: bzlib.h: No such file or directory Sep 04 04:56:29.677 INFO kablam! compilation terminated. Sep 04 04:56:29.677 INFO kablam! make: *** [cram/cram_io.o] Error 1 Sep 04 04:56:29.677 INFO kablam! thread 'main' panicked at 'failed to build htslib', build.rs:59:9 Sep 04 04:56:29.677 INFO kablam! stack backtrace: Sep 04 04:56:29.677 INFO kablam! 0: 0x55ea6b0e4b2e - std::sys::unix::backtrace::tracing::imp::unwind_backtrace::h583ed2894c1db4e8 Sep 04 04:56:29.677 INFO kablam! at libstd/sys/unix/backtrace/tracing/gcc_s.rs:49 Sep 04 04:56:29.678 INFO kablam! 1: 0x55ea6b0d3b66 - std::sys_common::backtrace::print::hb03c547ea490e9e5 Sep 04 04:56:29.678 INFO kablam! at libstd/sys_common/backtrace.rs:71 Sep 04 04:56:29.678 INFO kablam! at libstd/sys_common/backtrace.rs:59 Sep 04 04:56:29.678 INFO kablam! 2: 0x55ea6b0d1ecd - std::panicking::default_hook::{{closure}}::h74db1dbb754bb61b Sep 04 04:56:29.679 INFO kablam! at libstd/panicking.rs:211 Sep 04 04:56:29.679 INFO kablam! 3: 0x55ea6b0d1c40 - std::panicking::default_hook::h00b2b50b7c826057 Sep 04 04:56:29.679 INFO kablam! at libstd/panicking.rs:227 Sep 04 04:56:29.679 INFO kablam! 4: 0x55ea6b0d253c - std::panicking::rust_panic_with_hook::h82a465b5cd0f7696 Sep 04 04:56:29.679 INFO kablam! at libstd/panicking.rs:477 Sep 04 04:56:29.679 INFO kablam! 5: 0x55ea6b020fdf - std::panicking::begin_panic::h3ae242f200f1f64a Sep 04 04:56:29.679 INFO kablam! at /checkout/src/libstd/panicking.rs:411 Sep 04 04:56:29.679 INFO kablam! 6: 0x55ea6aaf6514 - build_script_build::main::hf9c50f0c739d280d Sep 04 04:56:29.679 INFO kablam! at /source/build.rs:59 Sep 04 04:56:29.679 INFO kablam! 7: 0x55ea6aaf763f - std::rt::lang_start::{{closure}}::h8b33987a5c923798 Sep 04 04:56:29.679 INFO kablam! at /checkout/src/libstd/rt.rs:74 Sep 04 04:56:29.679 INFO kablam! 8: 0x55ea6b0d1fd2 - std::panicking::try::do_call::hd86a9acb4a664678 Sep 04 04:56:29.679 INFO kablam! at libstd/rt.rs:59 Sep 04 04:56:29.679 INFO kablam! at libstd/panicking.rs:310 Sep 04 04:56:29.679 INFO kablam! 9: 0x55ea6b0f6cd9 - __rust_maybe_catch_panic Sep 04 04:56:29.679 INFO kablam! at libpanic_unwind/lib.rs:103 Sep 04 04:56:29.679 INFO kablam! 10: 0x55ea6b0df465 - std::rt::lang_start_internal::h8264bc6ad8e6b565 Sep 04 04:56:29.679 INFO kablam! at libstd/panicking.rs:289 Sep 04 04:56:29.679 INFO kablam! at libstd/panic.rs:392 Sep 04 04:56:29.679 INFO kablam! at libstd/rt.rs:58 Sep 04 04:56:29.679 INFO kablam! 11: 0x55ea6aaf7617 - std::rt::lang_start::he0748f4f5ca23f2b Sep 04 04:56:29.679 INFO kablam! at /checkout/src/libstd/rt.rs:74 Sep 04 04:56:29.679 INFO kablam! 12: 0x55ea6aaf69d9 - main Sep 04 04:56:29.679 INFO kablam! 13: 0x7f78616a882f - __libc_start_main Sep 04 04:56:29.679 INFO kablam! 14: 0x55ea6aaf5bc8 - _start Sep 04 04:56:29.679 INFO kablam! 15: 0x0 - Sep 04 04:56:29.679 INFO kablam! Sep 04 04:56:29.679 INFO kablam! su: No module specific data is present Sep 04 04:56:30.093 INFO running `"docker" "rm" "-f" "d20f51c5943e4854d9fd3bd24469513321f08a5531e5f52a4578a94d87931141"` Sep 04 04:56:30.189 INFO blam! d20f51c5943e4854d9fd3bd24469513321f08a5531e5f52a4578a94d87931141