Nov 27 23:51:58.994 INFO checking natir/mapping2barcode against master#0b9f19dff1347e29bf4362ab5a8fab84b43023b5 for pr-56074 Nov 27 23:51:58.994 INFO running `"docker" "create" "-v" "/mnt/big/crater/work/local/target-dirs/pr-56074/worker-4/master#0b9f19dff1347e29bf4362ab5a8fab84b43023b5:/target:rw,Z" "-v" "/mnt/big/crater/work/local/test-source/worker-4/pr-56074/master#0b9f19dff1347e29bf4362ab5a8fab84b43023b5:/source:ro,Z" "-v" "/mnt/big/crater/work/local/cargo-home:/cargo-home:ro,Z" "-v" "/mnt/big/crater/work/local/rustup-home:/rustup-home:ro,Z" "-e" "USER_ID=1000" "-e" "SOURCE_DIR=/source" "-e" "USER_ID=1000" "-e" "CMD=cargo +0b9f19dff1347e29bf4362ab5a8fab84b43023b5-alt check --frozen --all --all-targets" "-e" "CARGO_TARGET_DIR=/target" "-e" "CARGO_INCREMENTAL=0" "-e" "RUST_BACKTRACE=full" "-e" "RUSTFLAGS=--cap-lints=forbid" "-e" "CARGO_HOME=/cargo-home" "-e" "RUSTUP_HOME=/rustup-home" "-m" "1536M" "--network" "none" "crater"` Nov 27 23:51:59.360 INFO [stdout] b07c02a268b07bf00b87a85044240abac393651acc7bf023b2ef00622d86efb0 Nov 27 23:51:59.368 INFO running `"docker" "start" "-a" "b07c02a268b07bf00b87a85044240abac393651acc7bf023b2ef00622d86efb0"` Nov 27 23:52:00.755 INFO [stderr] usermod: no changes Nov 27 23:52:01.068 INFO [stderr] Compiling bindgen v0.36.1 Nov 27 23:52:01.074 INFO [stderr] Compiling bv v0.7.4 Nov 27 23:52:01.106 INFO [stderr] Checking ieee754 v0.2.2 Nov 27 23:52:01.122 INFO [stderr] Checking bytecount v0.3.2 Nov 27 23:52:01.128 INFO [stderr] Checking custom_derive v0.1.7 Nov 27 23:52:01.129 INFO [stderr] Checking linear-map v1.2.0 Nov 27 23:52:01.131 INFO [stderr] Checking ordermap v0.3.5 Nov 27 23:52:01.152 INFO [stderr] Checking fixedbitset v0.1.9 Nov 27 23:52:02.559 INFO [stderr] Compiling clang-sys v0.22.0 Nov 27 23:52:02.714 INFO [stderr] Compiling fs-utils v1.1.0 Nov 27 23:52:03.514 INFO [stderr] Compiling lzma-sys v0.1.11 Nov 27 23:52:04.996 INFO [stderr] Checking itertools v0.6.5 Nov 27 23:52:06.319 INFO [stderr] Compiling newtype_derive v0.1.6 Nov 27 23:52:06.389 INFO [stderr] Compiling libloading v0.5.0 Nov 27 23:52:08.454 INFO [stderr] Checking num-complex v0.1.43 Nov 27 23:52:08.457 INFO [stderr] Checking itertools-num v0.1.2 Nov 27 23:52:09.862 INFO [stderr] Compiling syn v0.15.14 Nov 27 23:52:09.942 INFO [stderr] Checking csv-core v0.1.4 Nov 27 23:52:10.121 INFO [stderr] Checking ordered-float v0.5.2 Nov 27 23:52:10.314 INFO [stderr] Checking petgraph v0.4.13 Nov 27 23:52:10.926 INFO [stderr] Compiling regex v1.0.5 Nov 27 23:52:14.733 INFO [stderr] Checking xz2 v0.1.6 Nov 27 23:52:18.517 INFO [stderr] Checking ndarray v0.9.1 Nov 27 23:52:42.175 INFO [stderr] Compiling env_logger v0.5.13 Nov 27 23:52:50.793 INFO [stderr] Compiling serde_derive v1.0.80 Nov 27 23:53:08.170 INFO [stderr] Compiling serde v1.0.80 Nov 27 23:53:20.668 INFO [stderr] Checking vec_map v0.8.1 Nov 27 23:53:20.668 INFO [stderr] Checking csv v1.0.2 Nov 27 23:53:20.668 INFO [stderr] Checking bio-types v0.4.0 Nov 27 23:53:20.668 INFO [stderr] Checking multimap v0.4.0 Nov 27 23:53:24.132 INFO [stderr] Checking clap v2.32.0 Nov 27 23:53:25.232 INFO [stderr] Checking bio v0.20.3 Nov 27 23:54:12.680 INFO [stderr] Compiling rust-htslib v0.21.0 Nov 27 23:54:40.941 INFO [stderr] error: failed to run custom build command for `rust-htslib v0.21.0` Nov 27 23:54:40.942 INFO [stderr] process didn't exit successfully: `/target/debug/build/rust-htslib-89fc87c4ae71d950/build-script-build` (exit code: 101) Nov 27 23:54:40.942 INFO [stderr] --- stdout Nov 27 23:54:40.942 INFO [stderr] echo '/* Default config.h generated by Makefile */' > config.h Nov 27 23:54:40.942 INFO [stderr] echo '#define HAVE_LIBBZ2 1' >> config.h Nov 27 23:54:40.943 INFO [stderr] echo '#define HAVE_LIBLZMA 1' >> config.h Nov 27 23:54:40.943 INFO [stderr] echo '#define HAVE_FSEEKO 1' >> config.h Nov 27 23:54:40.943 INFO [stderr] echo '#define HAVE_DRAND48 1' >> config.h Nov 27 23:54:40.944 INFO [stderr] gcc -g -Wall -O2 -fPIC -I. -c -o kfunc.o kfunc.c Nov 27 23:54:40.944 INFO [stderr] gcc -g -Wall -O2 -fPIC -I. -c -o knetfile.o knetfile.c Nov 27 23:54:40.944 INFO [stderr] gcc -g -Wall -O2 -fPIC -I. -c -o kstring.o kstring.c Nov 27 23:54:40.945 INFO [stderr] gcc -g -Wall -O2 -fPIC -I. -c -o bcf_sr_sort.o bcf_sr_sort.c Nov 27 23:54:40.945 INFO [stderr] gcc -g -Wall -O2 -fPIC -I. -c -o bgzf.o bgzf.c Nov 27 23:54:40.945 INFO [stderr] gcc -g -Wall -O2 -fPIC -I. -c -o errmod.o errmod.c Nov 27 23:54:40.945 INFO [stderr] gcc -g -Wall -O2 -fPIC -I. -c -o faidx.o faidx.c Nov 27 23:54:40.946 INFO [stderr] gcc -g -Wall -O2 -fPIC -I. -c -o hfile.o hfile.c Nov 27 23:54:40.946 INFO [stderr] gcc -g -Wall -O2 -fPIC -I. -c -o hfile_net.o hfile_net.c Nov 27 23:54:40.946 INFO [stderr] echo '#define HTS_VERSION "1.6"' > version.h Nov 27 23:54:40.947 INFO [stderr] gcc -g -Wall -O2 -fPIC -I. -c -o hts.o hts.c Nov 27 23:54:40.947 INFO [stderr] gcc -g -Wall -O2 -fPIC -I. -c -o hts_os.o hts_os.c Nov 27 23:54:40.947 INFO [stderr] gcc -g -Wall -O2 -fPIC -I. -c -o md5.o md5.c Nov 27 23:54:40.947 INFO [stderr] gcc -g -Wall -O2 -fPIC -I. -c -o multipart.o multipart.c Nov 27 23:54:40.948 INFO [stderr] gcc -g -Wall -O2 -fPIC -I. -c -o probaln.o probaln.c Nov 27 23:54:40.948 INFO [stderr] gcc -g -Wall -O2 -fPIC -I. -c -o realn.o realn.c Nov 27 23:54:40.948 INFO [stderr] gcc -g -Wall -O2 -fPIC -I. -c -o regidx.o regidx.c Nov 27 23:54:40.949 INFO [stderr] gcc -g -Wall -O2 -fPIC -I. -c -o sam.o sam.c Nov 27 23:54:40.949 INFO [stderr] gcc -g -Wall -O2 -fPIC -I. -c -o synced_bcf_reader.o synced_bcf_reader.c Nov 27 23:54:40.949 INFO [stderr] gcc -g -Wall -O2 -fPIC -I. -c -o vcf_sweep.o vcf_sweep.c Nov 27 23:54:40.950 INFO [stderr] gcc -g -Wall -O2 -fPIC -I. -c -o tbx.o tbx.c Nov 27 23:54:40.950 INFO [stderr] gcc -g -Wall -O2 -fPIC -I. -c -o textutils.o textutils.c Nov 27 23:54:40.950 INFO [stderr] gcc -g -Wall -O2 -fPIC -I. -c -o thread_pool.o thread_pool.c Nov 27 23:54:40.950 INFO [stderr] gcc -g -Wall -O2 -fPIC -I. -c -o vcf.o vcf.c Nov 27 23:54:40.951 INFO [stderr] gcc -g -Wall -O2 -fPIC -I. -c -o vcfutils.o vcfutils.c Nov 27 23:54:40.951 INFO [stderr] gcc -g -Wall -O2 -fPIC -I. -c -o cram/cram_codecs.o cram/cram_codecs.c Nov 27 23:54:40.951 INFO [stderr] gcc -g -Wall -O2 -fPIC -I. -c -o cram/cram_decode.o cram/cram_decode.c Nov 27 23:54:40.952 INFO [stderr] gcc -g -Wall -O2 -fPIC -I. -c -o cram/cram_encode.o cram/cram_encode.c Nov 27 23:54:40.952 INFO [stderr] gcc -g -Wall -O2 -fPIC -I. -c -o cram/cram_external.o cram/cram_external.c Nov 27 23:54:40.952 INFO [stderr] gcc -g -Wall -O2 -fPIC -I. -c -o cram/cram_index.o cram/cram_index.c Nov 27 23:54:40.953 INFO [stderr] gcc -g -Wall -O2 -fPIC -I. -c -o cram/cram_io.o cram/cram_io.c Nov 27 23:54:40.953 INFO [stderr] Makefile:120: recipe for target 'cram/cram_io.o' failed Nov 27 23:54:40.953 INFO [stderr] Nov 27 23:54:40.953 INFO [stderr] --- stderr Nov 27 23:54:40.954 INFO [stderr] cram/cram_io.c:57:19: fatal error: bzlib.h: No such file or directory Nov 27 23:54:40.954 INFO [stderr] compilation terminated. Nov 27 23:54:40.954 INFO [stderr] make: *** [cram/cram_io.o] Error 1 Nov 27 23:54:40.955 INFO [stderr] thread 'main' panicked at 'failed to build htslib', /cargo-home/registry/src/github.com-1ecc6299db9ec823/rust-htslib-0.21.0/build.rs:59:9 Nov 27 23:54:40.955 INFO [stderr] stack backtrace: Nov 27 23:54:40.955 INFO [stderr] 0: 0x564d0f3926c3 - std::sys::unix::backtrace::tracing::imp::unwind_backtrace::h7d972ccdbca3212d Nov 27 23:54:40.955 INFO [stderr] at libstd/sys/unix/backtrace/tracing/gcc_s.rs:49 Nov 27 23:54:40.956 INFO [stderr] 1: 0x564d0f38ce58 - std::sys_common::backtrace::_print::h2cdc7f13fc971a5c Nov 27 23:54:40.956 INFO [stderr] at libstd/sys_common/backtrace.rs:71 Nov 27 23:54:40.956 INFO [stderr] 2: 0x564d0f391634 - std::panicking::default_hook::{{closure}}::h0fb02fa5f239ab43 Nov 27 23:54:40.957 INFO [stderr] at libstd/sys_common/backtrace.rs:59 Nov 27 23:54:40.957 INFO [stderr] at libstd/panicking.rs:211 Nov 27 23:54:40.957 INFO [stderr] 3: 0x564d0f39139d - std::panicking::default_hook::h213e6465144a9cfa Nov 27 23:54:40.958 INFO [stderr] at libstd/panicking.rs:227 Nov 27 23:54:40.958 INFO [stderr] 4: 0x564d0f391d40 - std::panicking::rust_panic_with_hook::h8c5897af0a3d8b18 Nov 27 23:54:40.958 INFO [stderr] at libstd/panicking.rs:476 Nov 27 23:54:40.958 INFO [stderr] 5: 0x564d0f147c47 - std::panicking::begin_panic::h656c827bd8563ccb Nov 27 23:54:40.959 INFO [stderr] at /rustc/0b9f19dff1347e29bf4362ab5a8fab84b43023b5/src/libstd/panicking.rs:410 Nov 27 23:54:40.959 INFO [stderr] 6: 0x564d0ed8598b - build_script_build::main::h908e222b9713ec90 Nov 27 23:54:40.959 INFO [stderr] at /cargo-home/registry/src/github.com-1ecc6299db9ec823/rust-htslib-0.21.0/build.rs:59 Nov 27 23:54:40.960 INFO [stderr] 7: 0x564d0ed869af - std::rt::lang_start::{{closure}}::h3e21099611833ebe Nov 27 23:54:40.964 INFO [stderr] at /rustc/0b9f19dff1347e29bf4362ab5a8fab84b43023b5/src/libstd/rt.rs:74 Nov 27 23:54:40.964 INFO [stderr] 8: 0x564d0f391742 - std::panicking::try::do_call::h22e1d38891e16374 Nov 27 23:54:40.965 INFO [stderr] at libstd/rt.rs:59 Nov 27 23:54:40.965 INFO [stderr] at libstd/panicking.rs:310 Nov 27 23:54:40.965 INFO [stderr] 9: 0x564d0f3a5f29 - __rust_maybe_catch_panic Nov 27 23:54:40.966 INFO [stderr] at libpanic_unwind/lib.rs:102 Nov 27 23:54:40.966 INFO [stderr] 10: 0x564d0f392113 - std::rt::lang_start_internal::hdac97ccc132ce7ba Nov 27 23:54:40.966 INFO [stderr] at libstd/panicking.rs:289 Nov 27 23:54:40.966 INFO [stderr] at libstd/panic.rs:398 Nov 27 23:54:40.967 INFO [stderr] at libstd/rt.rs:58 Nov 27 23:54:40.967 INFO [stderr] 11: 0x564d0ed86988 - std::rt::lang_start::hf34dfbbeaf1a252b Nov 27 23:54:40.967 INFO [stderr] at /rustc/0b9f19dff1347e29bf4362ab5a8fab84b43023b5/src/libstd/rt.rs:74 Nov 27 23:54:40.967 INFO [stderr] 12: 0x564d0ed85e79 - main Nov 27 23:54:40.968 INFO [stderr] 13: 0x7f95c965482f - __libc_start_main Nov 27 23:54:40.968 INFO [stderr] 14: 0x564d0ed84fb8 - _start Nov 27 23:54:40.968 INFO [stderr] 15: 0x0 - Nov 27 23:54:40.969 INFO [stderr] Nov 27 23:54:40.969 INFO [stderr] su: No module specific data is present Nov 27 23:54:41.744 INFO running `"docker" "inspect" "b07c02a268b07bf00b87a85044240abac393651acc7bf023b2ef00622d86efb0"` Nov 27 23:54:42.081 INFO running `"docker" "rm" "-f" "b07c02a268b07bf00b87a85044240abac393651acc7bf023b2ef00622d86efb0"` Nov 27 23:54:42.321 INFO [stdout] b07c02a268b07bf00b87a85044240abac393651acc7bf023b2ef00622d86efb0