Sep 06 00:52:07.611 INFO checking rust-htslib-0.21.0 against master#1c2e17f4e3a2070a7f703f51e29c1c388ef703b6 for pr-53854 Sep 06 00:52:07.611 INFO running: cargo +1c2e17f4e3a2070a7f703f51e29c1c388ef703b6-alt check --frozen --all --all-targets Sep 06 00:52:07.611 INFO running `"docker" "create" "-v" "/home/ec2-user/crater/./work/local/test-source/worker-4/pr-53854/master#1c2e17f4e3a2070a7f703f51e29c1c388ef703b6:/source:ro,Z" "-v" "/home/ec2-user/crater/./work/local/target-dirs/pr-53854/worker-4/master#1c2e17f4e3a2070a7f703f51e29c1c388ef703b6:/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=1000" "-e" "CMD=cargo +1c2e17f4e3a2070a7f703f51e29c1c388ef703b6-alt check --frozen --all --all-targets" "-e" "CARGO_INCREMENTAL=0" "-e" "RUST_BACKTRACE=full" "-e" "RUSTFLAGS=--cap-lints=forbid" "-m" "2G" "crater"` Sep 06 00:52:07.871 INFO blam! 6da4219634364368b1828e484691c136a644f31e6f6b7f0aaaeeffcf73681899 Sep 06 00:52:07.872 INFO running `"docker" "start" "-a" "6da4219634364368b1828e484691c136a644f31e6f6b7f0aaaeeffcf73681899"` Sep 06 00:52:09.195 INFO kablam! usermod: no changes Sep 06 00:52:09.507 INFO kablam! Compiling bindgen v0.36.1 Sep 06 00:52:09.507 INFO kablam! Checking linear-map v1.2.0 Sep 06 00:52:09.507 INFO kablam! Checking ieee754 v0.2.2 Sep 06 00:52:09.507 INFO kablam! Compiling clang-sys v0.22.0 Sep 06 00:52:09.507 INFO kablam! Compiling fs-utils v1.1.0 Sep 06 00:52:09.512 INFO kablam! Compiling newtype_derive v0.1.6 Sep 06 00:52:09.512 INFO kablam! Checking bio-types v0.2.0 Sep 06 00:52:38.514 INFO kablam! Compiling rust-htslib v0.21.0 (file:///source) Sep 06 00:52:58.863 INFO kablam! error: failed to run custom build command for `rust-htslib v0.21.0 (file:///source)` Sep 06 00:52:58.863 INFO kablam! process didn't exit successfully: `/target/debug/build/rust-htslib-74e491a0af0df1f0/build-script-build` (exit code: 101) Sep 06 00:52:58.863 INFO kablam! --- stdout Sep 06 00:52:58.863 INFO kablam! echo '/* Default config.h generated by Makefile */' > config.h Sep 06 00:52:58.863 INFO kablam! echo '#define HAVE_LIBBZ2 1' >> config.h Sep 06 00:52:58.863 INFO kablam! echo '#define HAVE_LIBLZMA 1' >> config.h Sep 06 00:52:58.863 INFO kablam! echo '#define HAVE_FSEEKO 1' >> config.h Sep 06 00:52:58.863 INFO kablam! echo '#define HAVE_DRAND48 1' >> config.h Sep 06 00:52:58.863 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o kfunc.o kfunc.c Sep 06 00:52:58.863 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o knetfile.o knetfile.c Sep 06 00:52:58.863 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o kstring.o kstring.c Sep 06 00:52:58.863 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o bcf_sr_sort.o bcf_sr_sort.c Sep 06 00:52:58.863 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o bgzf.o bgzf.c Sep 06 00:52:58.863 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o errmod.o errmod.c Sep 06 00:52:58.863 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o faidx.o faidx.c Sep 06 00:52:58.863 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o hfile.o hfile.c Sep 06 00:52:58.863 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o hfile_net.o hfile_net.c Sep 06 00:52:58.863 INFO kablam! echo '#define HTS_VERSION "1.6"' > version.h Sep 06 00:52:58.863 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o hts.o hts.c Sep 06 00:52:58.863 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o hts_os.o hts_os.c Sep 06 00:52:58.863 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o md5.o md5.c Sep 06 00:52:58.863 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o multipart.o multipart.c Sep 06 00:52:58.863 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o probaln.o probaln.c Sep 06 00:52:58.863 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o realn.o realn.c Sep 06 00:52:58.863 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o regidx.o regidx.c Sep 06 00:52:58.863 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o sam.o sam.c Sep 06 00:52:58.863 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o synced_bcf_reader.o synced_bcf_reader.c Sep 06 00:52:58.863 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o vcf_sweep.o vcf_sweep.c Sep 06 00:52:58.863 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o tbx.o tbx.c Sep 06 00:52:58.863 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o textutils.o textutils.c Sep 06 00:52:58.863 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o thread_pool.o thread_pool.c Sep 06 00:52:58.863 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o vcf.o vcf.c Sep 06 00:52:58.863 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o vcfutils.o vcfutils.c Sep 06 00:52:58.863 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o cram/cram_codecs.o cram/cram_codecs.c Sep 06 00:52:58.863 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o cram/cram_decode.o cram/cram_decode.c Sep 06 00:52:58.863 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o cram/cram_encode.o cram/cram_encode.c Sep 06 00:52:58.863 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o cram/cram_external.o cram/cram_external.c Sep 06 00:52:58.863 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o cram/cram_index.o cram/cram_index.c Sep 06 00:52:58.863 INFO kablam! gcc -g -Wall -O2 -fPIC -I. -c -o cram/cram_io.o cram/cram_io.c Sep 06 00:52:58.863 INFO kablam! Makefile:120: recipe for target 'cram/cram_io.o' failed Sep 06 00:52:58.863 INFO kablam! Sep 06 00:52:58.863 INFO kablam! --- stderr Sep 06 00:52:58.863 INFO kablam! cram/cram_io.c:57:19: fatal error: bzlib.h: No such file or directory Sep 06 00:52:58.863 INFO kablam! compilation terminated. Sep 06 00:52:58.863 INFO kablam! make: *** [cram/cram_io.o] Error 1 Sep 06 00:52:58.863 INFO kablam! thread 'main' panicked at 'failed to build htslib', build.rs:59:9 Sep 06 00:52:58.863 INFO kablam! stack backtrace: Sep 06 00:52:58.863 INFO kablam! 0: 0x55ffd5f0f6ce - std::sys::unix::backtrace::tracing::imp::unwind_backtrace::h082e5fdf9aff33df Sep 06 00:52:58.863 INFO kablam! at libstd/sys/unix/backtrace/tracing/gcc_s.rs:49 Sep 06 00:52:58.863 INFO kablam! 1: 0x55ffd5efe7e6 - std::sys_common::backtrace::print::hef53554d827c8c8b Sep 06 00:52:58.864 INFO kablam! at libstd/sys_common/backtrace.rs:71 Sep 06 00:52:58.864 INFO kablam! at libstd/sys_common/backtrace.rs:59 Sep 06 00:52:58.864 INFO kablam! 2: 0x55ffd5efcb6d - std::panicking::default_hook::{{closure}}::h34861d43158e89b9 Sep 06 00:52:58.864 INFO kablam! at libstd/panicking.rs:211 Sep 06 00:52:58.864 INFO kablam! 3: 0x55ffd5efc8e0 - std::panicking::default_hook::h8898fb997741a086 Sep 06 00:52:58.864 INFO kablam! at libstd/panicking.rs:227 Sep 06 00:52:58.864 INFO kablam! 4: 0x55ffd5efd1dc - std::panicking::rust_panic_with_hook::h2a2e767b3fe52fcb Sep 06 00:52:58.864 INFO kablam! at libstd/panicking.rs:477 Sep 06 00:52:58.864 INFO kablam! 5: 0x55ffd5eb1e4f - std::panicking::begin_panic::h01b98d825a1214ee Sep 06 00:52:58.864 INFO kablam! at /checkout/src/libstd/panicking.rs:411 Sep 06 00:52:58.864 INFO kablam! 6: 0x55ffd5922424 - build_script_build::main::hb409665d093495ac Sep 06 00:52:58.864 INFO kablam! at /source/build.rs:59 Sep 06 00:52:58.864 INFO kablam! 7: 0x55ffd592354f - std::rt::lang_start::{{closure}}::hc1b5164d71e522d8 Sep 06 00:52:58.864 INFO kablam! at /checkout/src/libstd/rt.rs:74 Sep 06 00:52:58.864 INFO kablam! 8: 0x55ffd5efcc72 - std::panicking::try::do_call::hd6568c1e1325fac3 Sep 06 00:52:58.864 INFO kablam! at libstd/rt.rs:59 Sep 06 00:52:58.864 INFO kablam! at libstd/panicking.rs:310 Sep 06 00:52:58.864 INFO kablam! 9: 0x55ffd5f223a9 - __rust_maybe_catch_panic Sep 06 00:52:58.864 INFO kablam! at libpanic_unwind/lib.rs:103 Sep 06 00:52:58.864 INFO kablam! 10: 0x55ffd5f0a055 - std::rt::lang_start_internal::hf4a29d9afcf3f720 Sep 06 00:52:58.864 INFO kablam! at libstd/panicking.rs:289 Sep 06 00:52:58.864 INFO kablam! at libstd/panic.rs:392 Sep 06 00:52:58.864 INFO kablam! at libstd/rt.rs:58 Sep 06 00:52:58.864 INFO kablam! 11: 0x55ffd5923527 - std::rt::lang_start::h232bb242ef13763a Sep 06 00:52:58.864 INFO kablam! at /checkout/src/libstd/rt.rs:74 Sep 06 00:52:58.864 INFO kablam! 12: 0x55ffd59228e9 - main Sep 06 00:52:58.864 INFO kablam! 13: 0x7f2b8219f82f - __libc_start_main Sep 06 00:52:58.864 INFO kablam! 14: 0x55ffd5921ad8 - _start Sep 06 00:52:58.864 INFO kablam! 15: 0x0 - Sep 06 00:52:58.864 INFO kablam! Sep 06 00:52:58.864 INFO kablam! su: No module specific data is present Sep 06 00:52:59.583 INFO running `"docker" "rm" "-f" "6da4219634364368b1828e484691c136a644f31e6f6b7f0aaaeeffcf73681899"` Sep 06 00:52:59.674 INFO blam! 6da4219634364368b1828e484691c136a644f31e6f6b7f0aaaeeffcf73681899