Nov 27 23:51:58.759 INFO checking natir/mapping2barcode against try#db42d4dad33013eba11ef37342ad9f614e5652b8 for pr-56074 Nov 27 23:51:58.761 INFO running `"docker" "create" "-v" "/mnt/big/crater/work/local/target-dirs/pr-56074/worker-5/try#db42d4dad33013eba11ef37342ad9f614e5652b8:/target:rw,Z" "-v" "/mnt/big/crater/work/local/test-source/worker-5/pr-56074/try#db42d4dad33013eba11ef37342ad9f614e5652b8:/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 +db42d4dad33013eba11ef37342ad9f614e5652b8-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 23:51:59.301 INFO [stdout] 54357e3aec109a0af9989198a79c9615908c0827c5754b9af0d6ab43a1636d47 Nov 27 23:51:59.316 INFO running `"docker" "start" "-a" "54357e3aec109a0af9989198a79c9615908c0827c5754b9af0d6ab43a1636d47"` Nov 27 23:52:00.460 INFO [stderr] usermod: no changes Nov 27 23:52:00.832 INFO [stderr] Compiling bindgen v0.36.1 Nov 27 23:52:00.836 INFO [stderr] Compiling termcolor v1.0.4 Nov 27 23:52:00.852 INFO [stderr] Compiling ndarray v0.9.1 Nov 27 23:52:00.852 INFO [stderr] Compiling bv v0.7.4 Nov 27 23:52:00.860 INFO [stderr] Checking ieee754 v0.2.2 Nov 27 23:52:00.860 INFO [stderr] Checking bytecount v0.3.2 Nov 27 23:52:00.860 INFO [stderr] Compiling log v0.4.5 Nov 27 23:52:00.860 INFO [stderr] Compiling clang-sys v0.22.0 Nov 27 23:52:02.467 INFO [stderr] Compiling fs-utils v1.1.0 Nov 27 23:52:05.797 INFO [stderr] Compiling lzma-sys v0.1.11 Nov 27 23:52:05.804 INFO [stderr] Checking itertools v0.6.5 Nov 27 23:52:05.817 INFO [stderr] Checking fxhash v0.2.1 Nov 27 23:52:05.864 INFO [stderr] Checking petgraph v0.4.13 Nov 27 23:52:08.095 INFO [stderr] Compiling bzip2-sys v0.1.6 Nov 27 23:52:08.181 INFO [stderr] Compiling memchr v2.1.0 Nov 27 23:52:08.215 INFO [stderr] Compiling libloading v0.5.0 Nov 27 23:52:08.231 INFO [stderr] Compiling cexpr v0.2.3 Nov 27 23:52:10.984 INFO [stderr] Checking num-complex v0.1.43 Nov 27 23:52:11.044 INFO [stderr] Checking num-integer v0.1.39 Nov 27 23:52:12.930 INFO [stderr] Compiling syn v0.15.14 Nov 27 23:52:13.683 INFO [stderr] Checking csv-core v0.1.4 Nov 27 23:52:14.265 INFO [stderr] Compiling thread_local v0.3.6 Nov 27 23:52:18.516 INFO [stderr] Checking flate2 v1.0.4 Nov 27 23:52:18.528 INFO [stderr] Checking ordered-float v0.5.2 Nov 27 23:52:18.616 INFO [stderr] Checking enum_primitive v0.1.1 Nov 27 23:52:20.261 INFO [stderr] Compiling aho-corasick v0.6.8 Nov 27 23:52:20.774 INFO [stderr] Checking regex v0.2.11 Nov 27 23:52:28.970 INFO [stderr] Checking bzip2 v0.3.3 Nov 27 23:52:29.085 INFO [stderr] Compiling regex v1.0.5 Nov 27 23:52:29.325 INFO [stderr] Checking xz2 v0.1.6 Nov 27 23:52:52.249 INFO [stderr] Compiling serde_derive v1.0.80 Nov 27 23:53:05.244 INFO [stderr] Compiling env_logger v0.5.13 Nov 27 23:53:16.217 INFO [stderr] Compiling serde v1.0.80 Nov 27 23:53:29.708 INFO [stderr] Checking multimap v0.4.0 Nov 27 23:53:29.708 INFO [stderr] Checking bio-types v0.4.0 Nov 27 23:53:29.708 INFO [stderr] Checking vec_map v0.8.1 Nov 27 23:53:29.708 INFO [stderr] Checking csv v1.0.2 Nov 27 23:53:33.929 INFO [stderr] Checking clap v2.32.0 Nov 27 23:53:38.033 INFO [stderr] Checking bio v0.20.3 Nov 27 23:54:20.333 INFO [stderr] Compiling rust-htslib v0.21.0 Nov 27 23:54:48.518 INFO [stderr] error: failed to run custom build command for `rust-htslib v0.21.0` Nov 27 23:54:48.518 INFO [stderr] process didn't exit successfully: `/target/debug/build/rust-htslib-0b87d4f8aea6a861/build-script-build` (exit code: 101) Nov 27 23:54:48.518 INFO [stderr] --- stdout Nov 27 23:54:48.518 INFO [stderr] echo '/* Default config.h generated by Makefile */' > config.h Nov 27 23:54:48.518 INFO [stderr] echo '#define HAVE_LIBBZ2 1' >> config.h Nov 27 23:54:48.518 INFO [stderr] echo '#define HAVE_LIBLZMA 1' >> config.h Nov 27 23:54:48.518 INFO [stderr] echo '#define HAVE_FSEEKO 1' >> config.h Nov 27 23:54:48.518 INFO [stderr] echo '#define HAVE_DRAND48 1' >> config.h Nov 27 23:54:48.518 INFO [stderr] gcc -g -Wall -O2 -fPIC -I. -c -o kfunc.o kfunc.c Nov 27 23:54:48.518 INFO [stderr] gcc -g -Wall -O2 -fPIC -I. -c -o knetfile.o knetfile.c Nov 27 23:54:48.518 INFO [stderr] gcc -g -Wall -O2 -fPIC -I. -c -o kstring.o kstring.c Nov 27 23:54:48.518 INFO [stderr] gcc -g -Wall -O2 -fPIC -I. -c -o bcf_sr_sort.o bcf_sr_sort.c Nov 27 23:54:48.518 INFO [stderr] gcc -g -Wall -O2 -fPIC -I. -c -o bgzf.o bgzf.c Nov 27 23:54:48.518 INFO [stderr] gcc -g -Wall -O2 -fPIC -I. -c -o errmod.o errmod.c Nov 27 23:54:48.518 INFO [stderr] gcc -g -Wall -O2 -fPIC -I. -c -o faidx.o faidx.c Nov 27 23:54:48.518 INFO [stderr] gcc -g -Wall -O2 -fPIC -I. -c -o hfile.o hfile.c Nov 27 23:54:48.518 INFO [stderr] gcc -g -Wall -O2 -fPIC -I. -c -o hfile_net.o hfile_net.c Nov 27 23:54:48.518 INFO [stderr] echo '#define HTS_VERSION "1.6"' > version.h Nov 27 23:54:48.518 INFO [stderr] gcc -g -Wall -O2 -fPIC -I. -c -o hts.o hts.c Nov 27 23:54:48.518 INFO [stderr] gcc -g -Wall -O2 -fPIC -I. -c -o hts_os.o hts_os.c Nov 27 23:54:48.518 INFO [stderr] gcc -g -Wall -O2 -fPIC -I. -c -o md5.o md5.c Nov 27 23:54:48.518 INFO [stderr] gcc -g -Wall -O2 -fPIC -I. -c -o multipart.o multipart.c Nov 27 23:54:48.518 INFO [stderr] gcc -g -Wall -O2 -fPIC -I. -c -o probaln.o probaln.c Nov 27 23:54:48.518 INFO [stderr] gcc -g -Wall -O2 -fPIC -I. -c -o realn.o realn.c Nov 27 23:54:48.518 INFO [stderr] gcc -g -Wall -O2 -fPIC -I. -c -o regidx.o regidx.c Nov 27 23:54:48.518 INFO [stderr] gcc -g -Wall -O2 -fPIC -I. -c -o sam.o sam.c Nov 27 23:54:48.518 INFO [stderr] gcc -g -Wall -O2 -fPIC -I. -c -o synced_bcf_reader.o synced_bcf_reader.c Nov 27 23:54:48.518 INFO [stderr] gcc -g -Wall -O2 -fPIC -I. -c -o vcf_sweep.o vcf_sweep.c Nov 27 23:54:48.518 INFO [stderr] gcc -g -Wall -O2 -fPIC -I. -c -o tbx.o tbx.c Nov 27 23:54:48.518 INFO [stderr] gcc -g -Wall -O2 -fPIC -I. -c -o textutils.o textutils.c Nov 27 23:54:48.518 INFO [stderr] gcc -g -Wall -O2 -fPIC -I. -c -o thread_pool.o thread_pool.c Nov 27 23:54:48.518 INFO [stderr] gcc -g -Wall -O2 -fPIC -I. -c -o vcf.o vcf.c Nov 27 23:54:48.518 INFO [stderr] gcc -g -Wall -O2 -fPIC -I. -c -o vcfutils.o vcfutils.c Nov 27 23:54:48.518 INFO [stderr] gcc -g -Wall -O2 -fPIC -I. -c -o cram/cram_codecs.o cram/cram_codecs.c Nov 27 23:54:48.518 INFO [stderr] gcc -g -Wall -O2 -fPIC -I. -c -o cram/cram_decode.o cram/cram_decode.c Nov 27 23:54:48.518 INFO [stderr] gcc -g -Wall -O2 -fPIC -I. -c -o cram/cram_encode.o cram/cram_encode.c Nov 27 23:54:48.518 INFO [stderr] gcc -g -Wall -O2 -fPIC -I. -c -o cram/cram_external.o cram/cram_external.c Nov 27 23:54:48.518 INFO [stderr] gcc -g -Wall -O2 -fPIC -I. -c -o cram/cram_index.o cram/cram_index.c Nov 27 23:54:48.518 INFO [stderr] gcc -g -Wall -O2 -fPIC -I. -c -o cram/cram_io.o cram/cram_io.c Nov 27 23:54:48.518 INFO [stderr] Makefile:120: recipe for target 'cram/cram_io.o' failed Nov 27 23:54:48.518 INFO [stderr] Nov 27 23:54:48.518 INFO [stderr] --- stderr Nov 27 23:54:48.518 INFO [stderr] cram/cram_io.c:57:19: fatal error: bzlib.h: No such file or directory Nov 27 23:54:48.518 INFO [stderr] compilation terminated. Nov 27 23:54:48.518 INFO [stderr] make: *** [cram/cram_io.o] Error 1 Nov 27 23:54:48.518 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 23:54:48.518 INFO [stderr] stack backtrace: Nov 27 23:54:48.518 INFO [stderr] 0: 0x5571c543f983 - std::sys::unix::backtrace::tracing::imp::unwind_backtrace::hf827638fb5cf8ff9 Nov 27 23:54:48.518 INFO [stderr] at libstd/sys/unix/backtrace/tracing/gcc_s.rs:49 Nov 27 23:54:48.518 INFO [stderr] 1: 0x5571c543a118 - std::sys_common::backtrace::_print::hdb8bfcc9f904df5e Nov 27 23:54:48.518 INFO [stderr] at libstd/sys_common/backtrace.rs:71 Nov 27 23:54:48.518 INFO [stderr] 2: 0x5571c543e8f4 - std::panicking::default_hook::{{closure}}::h1b9c69ee93097572 Nov 27 23:54:48.518 INFO [stderr] at libstd/sys_common/backtrace.rs:59 Nov 27 23:54:48.518 INFO [stderr] at libstd/panicking.rs:211 Nov 27 23:54:48.518 INFO [stderr] 3: 0x5571c543e65d - std::panicking::default_hook::hb063deb6d3812fe8 Nov 27 23:54:48.518 INFO [stderr] at libstd/panicking.rs:227 Nov 27 23:54:48.518 INFO [stderr] 4: 0x5571c543f000 - std::panicking::rust_panic_with_hook::hd206188292d981ab Nov 27 23:54:48.518 INFO [stderr] at libstd/panicking.rs:476 Nov 27 23:54:48.518 INFO [stderr] 5: 0x5571c5244bf7 - std::panicking::begin_panic::h7b82998b7d7116e5 Nov 27 23:54:48.518 INFO [stderr] at /rustc/db42d4dad33013eba11ef37342ad9f614e5652b8/src/libstd/panicking.rs:410 Nov 27 23:54:48.518 INFO [stderr] 6: 0x5571c4e32a3b - build_script_build::main::h9a20c647b6a9d24b Nov 27 23:54:48.518 INFO [stderr] at /cargo-home/registry/src/github.com-1ecc6299db9ec823/rust-htslib-0.21.0/build.rs:59 Nov 27 23:54:48.518 INFO [stderr] 7: 0x5571c4e33a5f - std::rt::lang_start::{{closure}}::hc873ff3757d7b7f7 Nov 27 23:54:48.519 INFO [stderr] at /rustc/db42d4dad33013eba11ef37342ad9f614e5652b8/src/libstd/rt.rs:74 Nov 27 23:54:48.519 INFO [stderr] 8: 0x5571c543ea02 - std::panicking::try::do_call::hba45c39c5a26745c Nov 27 23:54:48.519 INFO [stderr] at libstd/rt.rs:59 Nov 27 23:54:48.519 INFO [stderr] at libstd/panicking.rs:310 Nov 27 23:54:48.519 INFO [stderr] 9: 0x5571c54531e9 - __rust_maybe_catch_panic Nov 27 23:54:48.519 INFO [stderr] at libpanic_unwind/lib.rs:102 Nov 27 23:54:48.519 INFO [stderr] 10: 0x5571c543f3d3 - std::rt::lang_start_internal::he405094b8bacbb22 Nov 27 23:54:48.519 INFO [stderr] at libstd/panicking.rs:289 Nov 27 23:54:48.519 INFO [stderr] at libstd/panic.rs:398 Nov 27 23:54:48.519 INFO [stderr] at libstd/rt.rs:58 Nov 27 23:54:48.519 INFO [stderr] 11: 0x5571c4e33a38 - std::rt::lang_start::h74f09d2d5a2c8585 Nov 27 23:54:48.519 INFO [stderr] at /rustc/db42d4dad33013eba11ef37342ad9f614e5652b8/src/libstd/rt.rs:74 Nov 27 23:54:48.519 INFO [stderr] 12: 0x5571c4e32f29 - main Nov 27 23:54:48.519 INFO [stderr] 13: 0x7f20b302382f - __libc_start_main Nov 27 23:54:48.519 INFO [stderr] 14: 0x5571c4e32068 - _start Nov 27 23:54:48.519 INFO [stderr] 15: 0x0 - Nov 27 23:54:48.519 INFO [stderr] Nov 27 23:54:48.519 INFO [stderr] su: No module specific data is present Nov 27 23:54:49.554 INFO running `"docker" "inspect" "54357e3aec109a0af9989198a79c9615908c0827c5754b9af0d6ab43a1636d47"` Nov 27 23:54:49.812 INFO running `"docker" "rm" "-f" "54357e3aec109a0af9989198a79c9615908c0827c5754b9af0d6ab43a1636d47"` Nov 27 23:54:50.122 INFO [stdout] 54357e3aec109a0af9989198a79c9615908c0827c5754b9af0d6ab43a1636d47