Aug 31 15:29:52.003 INFO checking rust-htslib-0.21.0 against master#d0d81b7fc1421859ba0218e8a437af29ae3b0967 for pr-53578 Aug 31 15:29:52.003 INFO running: cargo +d0d81b7fc1421859ba0218e8a437af29ae3b0967-alt check --frozen --all --all-targets Aug 31 15:29:52.004 INFO running `"docker" "create" "-v" "/home/ec2-user/crater/./work/local/test-source/worker-3/pr-53578/master#d0d81b7fc1421859ba0218e8a437af29ae3b0967:/source:ro,Z" "-v" "/home/ec2-user/crater/./work/local/target-dirs/pr-53578/worker-3/master#d0d81b7fc1421859ba0218e8a437af29ae3b0967:/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 +d0d81b7fc1421859ba0218e8a437af29ae3b0967-alt check --frozen --all --all-targets" "-e" "CARGO_INCREMENTAL=0" "-e" "RUST_BACKTRACE=full" "-e" "RUSTFLAGS=--cap-lints=forbid" "-m" "2G" "crater"` Aug 31 15:29:52.229 INFO blam! 5437fb37b865d839927f2e35537eff0e891e2c20f5e49abea4cdb21802722e98 Aug 31 15:29:52.231 INFO running `"docker" "start" "-a" "5437fb37b865d839927f2e35537eff0e891e2c20f5e49abea4cdb21802722e98"` Aug 31 15:29:53.085 INFO kablam! Checking ieee754 v0.2.2 Aug 31 15:29:53.085 INFO kablam! Checking linear-map v1.2.0 Aug 31 15:29:53.088 INFO kablam! Compiling fs-utils v1.1.0 Aug 31 15:29:53.092 INFO kablam! Checking bio-types v0.2.0 Aug 31 15:29:54.512 INFO kablam! Compiling rust-htslib v0.21.0 (file:///source) Aug 31 15:30:17.770 INFO kablam! error: failed to run custom build command for `rust-htslib v0.21.0 (file:///source)` Aug 31 15:30:17.770 INFO kablam! process didn't exit successfully: `/target/debug/build/rust-htslib-14d45f265003b518/build-script-build` (exit code: 101) Aug 31 15:30:17.770 INFO kablam! --- stdout Aug 31 15:30:17.770 INFO kablam! echo '/* Default config.h generated by Makefile */' > config.h Aug 31 15:30:17.771 INFO kablam! echo '#define HAVE_LIBBZ2 1' >> config.h Aug 31 15:30:17.771 INFO kablam! echo '#define HAVE_LIBLZMA 1' >> config.h Aug 31 15:30:17.771 INFO kablam! echo '#define HAVE_FSEEKO 1' >> config.h Aug 31 15:30:17.771 INFO kablam! echo '#define HAVE_DRAND48 1' >> config.h Aug 31 15:30:17.771 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o kfunc.o kfunc.c Aug 31 15:30:17.771 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o knetfile.o knetfile.c Aug 31 15:30:17.771 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o kstring.o kstring.c Aug 31 15:30:17.771 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o bcf_sr_sort.o bcf_sr_sort.c Aug 31 15:30:17.771 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o bgzf.o bgzf.c Aug 31 15:30:17.771 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o errmod.o errmod.c Aug 31 15:30:17.771 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o faidx.o faidx.c Aug 31 15:30:17.771 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o hfile.o hfile.c Aug 31 15:30:17.771 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o hfile_net.o hfile_net.c Aug 31 15:30:17.771 INFO kablam! echo '#define HTS_VERSION "1.6"' > version.h Aug 31 15:30:17.771 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o hts.o hts.c Aug 31 15:30:17.771 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o hts_os.o hts_os.c Aug 31 15:30:17.771 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o md5.o md5.c Aug 31 15:30:17.771 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o multipart.o multipart.c Aug 31 15:30:17.771 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o probaln.o probaln.c Aug 31 15:30:17.771 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o realn.o realn.c Aug 31 15:30:17.772 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o regidx.o regidx.c Aug 31 15:30:17.772 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o sam.o sam.c Aug 31 15:30:17.772 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o synced_bcf_reader.o synced_bcf_reader.c Aug 31 15:30:17.772 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o vcf_sweep.o vcf_sweep.c Aug 31 15:30:17.772 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o tbx.o tbx.c Aug 31 15:30:17.772 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o textutils.o textutils.c Aug 31 15:30:17.772 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o thread_pool.o thread_pool.c Aug 31 15:30:17.772 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o vcf.o vcf.c Aug 31 15:30:17.772 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o vcfutils.o vcfutils.c Aug 31 15:30:17.772 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o cram/cram_codecs.o cram/cram_codecs.c Aug 31 15:30:17.772 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o cram/cram_decode.o cram/cram_decode.c Aug 31 15:30:17.772 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o cram/cram_encode.o cram/cram_encode.c Aug 31 15:30:17.772 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o cram/cram_external.o cram/cram_external.c Aug 31 15:30:17.772 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o cram/cram_index.o cram/cram_index.c Aug 31 15:30:17.772 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o cram/cram_io.o cram/cram_io.c Aug 31 15:30:17.772 INFO kablam! Makefile:120: recipe for target 'cram/cram_io.o' failed Aug 31 15:30:17.772 INFO kablam! Aug 31 15:30:17.772 INFO kablam! --- stderr Aug 31 15:30:17.772 INFO kablam! cram/cram_io.c:57:19: fatal error: bzlib.h: No such file or directory Aug 31 15:30:17.773 INFO kablam! compilation terminated. Aug 31 15:30:17.773 INFO kablam! make: *** [cram/cram_io.o] Error 1 Aug 31 15:30:17.773 INFO kablam! thread 'main' panicked at 'failed to build htslib', build.rs:59:9 Aug 31 15:30:17.773 INFO kablam! stack backtrace: Aug 31 15:30:17.773 INFO kablam! 0: 0x564420a7f14e - std::sys::unix::backtrace::tracing::imp::unwind_backtrace::h8c3d0a2d42413513 Aug 31 15:30:17.773 INFO kablam! at libstd/sys/unix/backtrace/tracing/gcc_s.rs:49 Aug 31 15:30:17.773 INFO kablam! 1: 0x564420a6e2c6 - std::sys_common::backtrace::print::h2501b31339c3d559 Aug 31 15:30:17.773 INFO kablam! at libstd/sys_common/backtrace.rs:71 Aug 31 15:30:17.773 INFO kablam! at libstd/sys_common/backtrace.rs:59 Aug 31 15:30:17.773 INFO kablam! 2: 0x564420a6c5fd - std::panicking::default_hook::{{closure}}::h9550b067844d79de Aug 31 15:30:17.773 INFO kablam! at libstd/panicking.rs:211 Aug 31 15:30:17.773 INFO kablam! 3: 0x564420a6c370 - std::panicking::default_hook::h26bd688683b20acb Aug 31 15:30:17.773 INFO kablam! at libstd/panicking.rs:227 Aug 31 15:30:17.773 INFO kablam! 4: 0x564420a6cc6c - std::panicking::rust_panic_with_hook::h0967a90ee06b4501 Aug 31 15:30:17.773 INFO kablam! at libstd/panicking.rs:475 Aug 31 15:30:17.773 INFO kablam! 5: 0x5644208a6def - std::panicking::begin_panic::h1154d03888c27ab2 Aug 31 15:30:17.773 INFO kablam! at /checkout/src/libstd/panicking.rs:409 Aug 31 15:30:17.773 INFO kablam! 6: 0x564420490458 - build_script_build::main::hbeea7441bb40e7f0 Aug 31 15:30:17.773 INFO kablam! at /source/build.rs:59 Aug 31 15:30:17.773 INFO kablam! 7: 0x56442049158f - std::rt::lang_start::{{closure}}::hf80a4941feb90ef7 Aug 31 15:30:17.773 INFO kablam! at /checkout/src/libstd/rt.rs:74 Aug 31 15:30:17.773 INFO kablam! 8: 0x564420a6c702 - std::panicking::try::do_call::hc4206115bb2011fe Aug 31 15:30:17.773 INFO kablam! at libstd/rt.rs:59 Aug 31 15:30:17.773 INFO kablam! at libstd/panicking.rs:310 Aug 31 15:30:17.773 INFO kablam! 9: 0x564420a90da9 - __rust_maybe_catch_panic Aug 31 15:30:17.773 INFO kablam! at libpanic_unwind/lib.rs:102 Aug 31 15:30:17.773 INFO kablam! 10: 0x564420a79ac5 - std::rt::lang_start_internal::h0f4e93d8d2604488 Aug 31 15:30:17.773 INFO kablam! at libstd/panicking.rs:289 Aug 31 15:30:17.773 INFO kablam! at libstd/panic.rs:392 Aug 31 15:30:17.773 INFO kablam! at libstd/rt.rs:58 Aug 31 15:30:17.774 INFO kablam! 11: 0x564420491567 - std::rt::lang_start::ha80a1fd5c9ee4fc6 Aug 31 15:30:17.774 INFO kablam! at /checkout/src/libstd/rt.rs:74 Aug 31 15:30:17.774 INFO kablam! 12: 0x564420490929 - main Aug 31 15:30:17.774 INFO kablam! 13: 0x7f808eedc82f - __libc_start_main Aug 31 15:30:17.774 INFO kablam! 14: 0x56442048fad8 - _start Aug 31 15:30:17.774 INFO kablam! 15: 0x0 - Aug 31 15:30:17.774 INFO kablam! Aug 31 15:30:17.774 INFO kablam! su: No module specific data is present Aug 31 15:30:18.135 INFO running `"docker" "rm" "-f" "5437fb37b865d839927f2e35537eff0e891e2c20f5e49abea4cdb21802722e98"` Aug 31 15:30:18.248 INFO blam! 5437fb37b865d839927f2e35537eff0e891e2c20f5e49abea4cdb21802722e98