[INFO] cloning repository https://github.com/mal2017/tcq [INFO] running `Command { std: "git" "-c" "credential.helper=" "-c" "credential.helper=/workspace/cargo-home/bin/git-credential-null" "clone" "--bare" "https://github.com/mal2017/tcq" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fmal2017%2Ftcq", kill_on_drop: false }` [INFO] [stderr] Cloning into bare repository '/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fmal2017%2Ftcq'... [INFO] running `Command { std: "git" "rev-parse" "HEAD", kill_on_drop: false }` [INFO] [stdout] 8f1d6f947f2d7e33eec738ba82cec4875b4e4f4f [INFO] testing mal2017/tcq against master#d98a5da813da67eb189387b8ccfb73cf481275d8+rustflags=-Copt-level=3 for pr-138759-retry [INFO] running `Command { std: "git" "clone" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fmal2017%2Ftcq" "/workspace/builds/worker-6-tc1/source", kill_on_drop: false }` [INFO] [stderr] Cloning into '/workspace/builds/worker-6-tc1/source'... [INFO] [stderr] done. [INFO] started tweaking git repo https://github.com/mal2017/tcq [INFO] finished tweaking git repo https://github.com/mal2017/tcq [INFO] tweaked toml for git repo https://github.com/mal2017/tcq written to /workspace/builds/worker-6-tc1/source/Cargo.toml [INFO] validating manifest of git repo https://github.com/mal2017/tcq on toolchain d98a5da813da67eb189387b8ccfb73cf481275d8 [INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+d98a5da813da67eb189387b8ccfb73cf481275d8" "metadata" "--manifest-path" "Cargo.toml" "--no-deps", kill_on_drop: false }` [INFO] crate git repo https://github.com/mal2017/tcq already has a lockfile, it will not be regenerated [INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+d98a5da813da67eb189387b8ccfb73cf481275d8" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }` [INFO] [stderr] warning: no edition set: defaulting to the 2015 edition while the latest is 2024 [INFO] [stderr] Updating crates.io index [INFO] [stderr] Updating git repository `https://github.com/rust-bio/rust-htslib.git` [INFO] [stderr] Updating git submodule `https://github.com/samtools/htslib.git` [INFO] [stderr] Downloading crates ... [INFO] [stderr] Downloaded quote v0.6.12 [INFO] [stderr] Downloaded smallvec v0.6.9 [INFO] [stderr] Downloaded utf8-ranges v1.0.2 [INFO] [stderr] Downloaded serde_derive v1.0.90 [INFO] [stderr] Downloaded termcolor v1.0.4 [INFO] [stderr] Downloaded unicode-normalization v0.1.8 [INFO] [stderr] Downloaded num-complex v0.1.43 [INFO] [stderr] Downloaded libloading v0.5.0 [INFO] [stderr] Downloaded indicatif v0.11.0 [INFO] [stderr] Downloaded ordered-float v1.0.2 [INFO] [stderr] Downloaded bit-vec v0.5.1 [INFO] [stderr] Downloaded rustc_version v0.1.7 [INFO] [stderr] Downloaded bit-set v0.5.1 [INFO] [stderr] Downloaded bv v0.10.0 [INFO] [stderr] Downloaded rayon-core v1.4.1 [INFO] [stderr] Downloaded backtrace-sys v0.1.28 [INFO] [stderr] Downloaded itertools v0.7.11 [INFO] [stderr] Downloaded ndarray v0.12.1 [INFO] [stderr] Downloaded bio v0.25.0 [INFO] [stderr] Downloaded itertools v0.8.0 [INFO] [stderr] Downloaded statrs v0.9.0 [INFO] [stderr] Downloaded rayon v1.0.3 [INFO] [stderr] Downloaded serde_json v1.0.39 [INFO] [stderr] Downloaded winapi v0.3.7 [INFO] [stderr] Downloaded csv v1.0.7 [INFO] [stderr] Downloaded libz-sys v1.0.25 [INFO] [stderr] Downloaded bindgen v0.49.0 [INFO] [stderr] Downloaded itertools v0.6.5 [INFO] [stderr] Downloaded regex-syntax v0.6.6 [INFO] [stderr] Downloaded parking_lot v0.7.1 [INFO] [stderr] Downloaded failure v0.1.5 [INFO] [stderr] Downloaded bio-types v0.5.1 [INFO] [stderr] Downloaded cc v1.0.36 [INFO] [stderr] Downloaded rand_jitter v0.1.3 [INFO] [stderr] Downloaded bzip2-sys v0.1.7 [INFO] [stderr] Downloaded lzma-sys v0.1.14 [INFO] [stderr] Downloaded fs-utils v1.1.0 [INFO] [stderr] Downloaded proc-macro2 v0.4.29 [INFO] [stderr] Downloaded clang-sys v0.28.0 [INFO] [stderr] Downloaded libc v0.2.53 [INFO] [stderr] Downloaded syn v0.15.33 [INFO] [stderr] Downloaded serde v1.0.90 [INFO] [stderr] Downloaded rand_core v0.4.0 [INFO] [stderr] Downloaded parking_lot_core v0.4.0 [INFO] [stderr] Downloaded either v1.5.2 [INFO] [stderr] Downloaded semver v0.1.20 [INFO] [stderr] Downloaded newtype_derive v0.1.6 [INFO] [stderr] Downloaded ucd-util v0.1.3 [INFO] [stderr] Downloaded bytecount v0.3.2 [INFO] [stderr] Downloaded itertools-num v0.1.3 [INFO] [stderr] Downloaded multimap v0.4.0 [INFO] [stderr] Downloaded nodrop v0.1.13 [INFO] [stderr] Downloaded ryu v0.2.7 [INFO] [stderr] Downloaded encode_unicode v0.3.5 [INFO] [stderr] Downloaded console v0.7.5 [INFO] [stderr] Downloaded which v2.0.1 [INFO] [stderr] Downloaded memchr v2.2.0 [INFO] [stderr] Downloaded num-complex v0.2.1 [INFO] [stderr] Downloaded num-integer v0.1.39 [INFO] [stderr] Downloaded same-file v1.0.4 [INFO] [stderr] Downloaded itoa v0.4.3 [INFO] [stderr] Downloaded clicolors-control v1.0.0 [INFO] [stderr] Downloaded number_prefix v0.2.8 [INFO] [stderr] Downloaded ndarray v0.11.2 [INFO] [stderr] Downloaded vcpkg v0.2.6 [INFO] [stderr] Downloaded pkg-config v0.3.14 [INFO] [stderr] Downloaded aho-corasick v0.7.3 [INFO] [stderr] Downloaded cast v0.2.2 [INFO] [stderr] Downloaded arrayvec v0.4.10 [INFO] [stderr] Downloaded crossbeam-epoch v0.3.1 [INFO] [stderr] Downloaded crossbeam-utils v0.2.2 [INFO] [stderr] Downloaded crossbeam-deque v0.2.0 [INFO] [stderr] Downloaded num_cpus v1.10.0 [INFO] [stderr] Downloaded tinytemplate v1.0.1 [INFO] [stderr] Downloaded walkdir v2.2.7 [INFO] [stderr] Downloaded csv-core v0.1.5 [INFO] [stderr] Downloaded owning_ref v0.4.0 [INFO] [stderr] Downloaded matrixmultiply v0.1.15 [INFO] [stderr] Downloaded lazy_static v1.3.0 [INFO] [stderr] Downloaded rawpointer v0.1.0 [INFO] [stderr] Downloaded num-traits v0.2.6 [INFO] [stderr] Downloaded cexpr v0.3.5 [INFO] [stderr] Downloaded redox_syscall v0.1.54 [INFO] [stderr] Downloaded termion v1.5.2 [INFO] [stderr] Downloaded wincolor v1.0.1 [INFO] [stderr] Downloaded env_logger v0.6.1 [INFO] [stderr] Downloaded hashbrown v0.1.8 [INFO] [stderr] Downloaded log v0.4.6 [INFO] [stderr] Downloaded autocfg v0.1.2 [INFO] [stderr] Downloaded rustc-demangle v0.1.14 [INFO] [stderr] Downloaded yaml-rust v0.3.5 [INFO] [stderr] Downloaded byteorder v1.3.1 [INFO] [stderr] Downloaded cfg-if v0.1.7 [INFO] [stderr] Downloaded backtrace v0.3.15 [INFO] [stderr] Downloaded regex v1.1.6 [INFO] [stderr] Downloaded numtoa v0.1.0 [INFO] [stderr] Downloaded humantime v1.2.0 [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-6-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-6-tc1/source:/opt/rustwide/workdir:ro,Z" "-v" "/var/lib/crater-agent-workspace/cargo-home:/opt/rustwide/cargo-home:ro,Z" "-v" "/var/lib/crater-agent-workspace/rustup-home:/opt/rustwide/rustup-home:ro,Z" "-e" "SOURCE_DIR=/opt/rustwide/workdir" "-e" "CARGO_TARGET_DIR=/opt/rustwide/target" "-e" "CARGO_HOME=/opt/rustwide/cargo-home" "-e" "RUSTUP_HOME=/opt/rustwide/rustup-home" "-w" "/opt/rustwide/workdir" "-m" "1610612736" "--user" "0:0" "--network" "none" "ghcr.io/rust-lang/crates-build-env/linux@sha256:e90291280db7d1fac5b66fc6dad9f9662629e7365a55743daf9bdf73ebc4ea79" "/opt/rustwide/cargo-home/bin/cargo" "+d98a5da813da67eb189387b8ccfb73cf481275d8" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }` [INFO] [stdout] f2b7a0e69fc4845befe37e01ae9c5afbb5c830bbb720f81c9de4816aff981eaa [INFO] running `Command { std: "docker" "start" "-a" "f2b7a0e69fc4845befe37e01ae9c5afbb5c830bbb720f81c9de4816aff981eaa", kill_on_drop: false }` [INFO] running `Command { std: "docker" "inspect" "f2b7a0e69fc4845befe37e01ae9c5afbb5c830bbb720f81c9de4816aff981eaa", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "f2b7a0e69fc4845befe37e01ae9c5afbb5c830bbb720f81c9de4816aff981eaa", kill_on_drop: false }` [INFO] [stdout] f2b7a0e69fc4845befe37e01ae9c5afbb5c830bbb720f81c9de4816aff981eaa [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-6-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-6-tc1/source:/opt/rustwide/workdir:ro,Z" "-v" "/var/lib/crater-agent-workspace/cargo-home:/opt/rustwide/cargo-home:ro,Z" "-v" "/var/lib/crater-agent-workspace/rustup-home:/opt/rustwide/rustup-home:ro,Z" "-e" "SOURCE_DIR=/opt/rustwide/workdir" "-e" "CARGO_TARGET_DIR=/opt/rustwide/target" "-e" "CARGO_INCREMENTAL=0" "-e" "RUST_BACKTRACE=full" "-e" "RUSTFLAGS=--cap-lints=forbid -Copt-level=3" "-e" "RUSTDOCFLAGS=--cap-lints=forbid" "-e" "CARGO_HOME=/opt/rustwide/cargo-home" "-e" "RUSTUP_HOME=/opt/rustwide/rustup-home" "-w" "/opt/rustwide/workdir" "-m" "1610612736" "--user" "0:0" "--network" "none" "ghcr.io/rust-lang/crates-build-env/linux@sha256:e90291280db7d1fac5b66fc6dad9f9662629e7365a55743daf9bdf73ebc4ea79" "/opt/rustwide/cargo-home/bin/cargo" "+d98a5da813da67eb189387b8ccfb73cf481275d8" "build" "--frozen" "--message-format=json", kill_on_drop: false }` [INFO] [stdout] 5a3706d4848c59c9b495a19f8306719ee37bbf078b9696d4948d56e1901e0245 [INFO] running `Command { std: "docker" "start" "-a" "5a3706d4848c59c9b495a19f8306719ee37bbf078b9696d4948d56e1901e0245", kill_on_drop: false }` [INFO] [stderr] warning: no edition set: defaulting to the 2015 edition while the latest is 2024 [INFO] [stderr] Compiling libc v0.2.53 [INFO] [stderr] Compiling cc v1.0.36 [INFO] [stderr] Compiling autocfg v0.1.2 [INFO] [stderr] Compiling memchr v2.2.0 [INFO] [stderr] Compiling proc-macro2 v0.4.29 [INFO] [stderr] Compiling syn v0.15.33 [INFO] [stderr] Compiling serde v1.0.90 [INFO] [stderr] Compiling num-traits v0.2.6 [INFO] [stderr] Compiling lazy_static v1.3.0 [INFO] [stderr] Compiling rand_core v0.4.0 [INFO] [stderr] Compiling ucd-util v0.1.3 [INFO] [stderr] Compiling regex v1.1.6 [INFO] [stderr] Compiling utf8-ranges v1.0.2 [INFO] [stderr] Compiling cfg-if v0.1.7 [INFO] [stderr] Compiling quick-error v1.2.2 [INFO] [stderr] Compiling scopeguard v0.3.3 [INFO] [stderr] Compiling byteorder v1.3.1 [INFO] [stderr] Compiling thread_local v0.3.6 [INFO] [stderr] Compiling regex-syntax v0.6.6 [INFO] [stderr] Compiling smallvec v0.6.9 [INFO] [stderr] Compiling rand_core v0.3.1 [INFO] [stderr] Compiling glob v0.2.11 [INFO] [stderr] Compiling unicode-width v0.1.5 [INFO] [stderr] Compiling pkg-config v0.3.14 [INFO] [stderr] Compiling nom v4.2.3 [INFO] [stderr] Compiling backtrace v0.3.15 [INFO] [stderr] Compiling rand_chacha v0.1.1 [INFO] [stderr] Compiling rand_pcg v0.1.2 [INFO] [stderr] Compiling rustc-demangle v0.1.14 [INFO] [stderr] Compiling rand v0.6.5 [INFO] [stderr] Compiling humantime v1.2.0 [INFO] [stderr] Compiling log v0.4.6 [INFO] [stderr] Compiling semver v0.1.20 [INFO] [stderr] Compiling termcolor v1.0.4 [INFO] [stderr] Compiling either v1.5.2 [INFO] [stderr] Compiling parking_lot_core v0.4.0 [INFO] [stderr] Compiling textwrap v0.10.0 [INFO] [stderr] Compiling atty v0.2.11 [INFO] [stderr] Compiling rustc_version v0.1.7 [INFO] [stderr] Compiling rand_os v0.1.3 [INFO] [stderr] Compiling rand_isaac v0.1.1 [INFO] [stderr] Compiling rand_hc v0.1.0 [INFO] [stderr] Compiling rand_xorshift v0.1.1 [INFO] [stderr] Compiling rand_jitter v0.1.3 [INFO] [stderr] Compiling quote v0.6.12 [INFO] [stderr] Compiling aho-corasick v0.7.3 [INFO] [stderr] Compiling matrixmultiply v0.1.15 [INFO] [stderr] Compiling ansi_term v0.11.0 [INFO] [stderr] Compiling yaml-rust v0.3.5 [INFO] [stderr] Compiling strsim v0.7.0 [INFO] [stderr] Compiling bindgen v0.49.0 [INFO] [stderr] Compiling clang-sys v0.28.0 [INFO] [stderr] Compiling bitflags v1.0.4 [INFO] [stderr] Compiling stable_deref_trait v1.1.1 [INFO] [stderr] Compiling newtype_derive v0.1.6 [INFO] [stderr] Compiling owning_ref v0.4.0 [INFO] [stderr] Compiling hashbrown v0.1.8 [INFO] [stderr] Compiling num-complex v0.2.1 [INFO] [stderr] Compiling rawpointer v0.1.0 [INFO] [stderr] Compiling peeking_take_while v0.1.2 [INFO] [stderr] Compiling ryu v0.2.7 [INFO] [stderr] Compiling shlex v0.1.1 [INFO] [stderr] Compiling lock_api v0.1.5 [INFO] [stderr] Compiling bv v0.10.0 [INFO] [stderr] Compiling rand v0.4.6 [INFO] [stderr] Compiling itertools v0.7.11 [INFO] [stderr] Compiling unicode-normalization v0.1.8 [INFO] [stderr] Compiling fs-utils v1.1.0 [INFO] [stderr] Compiling cexpr v0.3.5 [INFO] [stderr] Compiling num-integer v0.1.39 [INFO] [stderr] Compiling ndarray v0.12.1 [INFO] [stderr] Compiling csv-core v0.1.5 [INFO] [stderr] Compiling rand v0.3.23 [INFO] [stderr] Compiling clicolors-control v1.0.0 [INFO] [stderr] Compiling termios v0.3.1 [INFO] [stderr] Compiling ndarray v0.11.2 [INFO] [stderr] Compiling itoa v0.4.3 [INFO] [stderr] Compiling bio v0.25.0 [INFO] [stderr] Compiling custom_derive v0.1.7 [INFO] [stderr] Compiling bit-vec v0.5.1 [INFO] [stderr] Compiling statrs v0.9.0 [INFO] [stderr] Compiling bit-set v0.5.1 [INFO] [stderr] Compiling fxhash v0.2.1 [INFO] [stderr] Compiling idna v0.1.5 [INFO] [stderr] Compiling ordered-float v1.0.2 [INFO] [stderr] Compiling itertools-num v0.1.3 [INFO] [stderr] Compiling approx v0.3.2 [INFO] [stderr] Compiling number_prefix v0.2.8 [INFO] [stderr] Compiling num-traits v0.1.43 [INFO] [stderr] Compiling num-complex v0.1.43 [INFO] [stderr] Compiling itertools v0.6.5 [INFO] [stderr] Compiling linear-map v1.2.0 [INFO] [stderr] Compiling lazy_static v0.2.11 [INFO] [stderr] Compiling url v1.7.2 [INFO] [stderr] Compiling parking_lot v0.7.1 [INFO] [stderr] Compiling bitflags v0.9.1 [INFO] [stderr] Compiling ieee754 v0.2.6 [INFO] [stderr] Compiling bytecount v0.3.2 [INFO] [stderr] Compiling backtrace-sys v0.1.28 [INFO] [stderr] Compiling libloading v0.5.0 [INFO] [stderr] Compiling bzip2-sys v0.1.7 [INFO] [stderr] Compiling lzma-sys v0.1.14 [INFO] [stderr] Compiling libz-sys v1.0.25 [INFO] [stderr] Compiling env_logger v0.6.1 [INFO] [stderr] Compiling console v0.7.5 [INFO] [stderr] Compiling env_logger v0.5.13 [INFO] [stderr] Compiling indicatif v0.11.0 [INFO] [stderr] Compiling failure v0.1.5 [INFO] [stderr] Compiling which v2.0.1 [INFO] [stderr] Compiling serde_derive v1.0.90 [INFO] [stderr] Compiling vec_map v0.8.1 [INFO] [stderr] Compiling bio-types v0.5.1 [INFO] [stderr] Compiling csv v1.0.7 [INFO] [stderr] Compiling multimap v0.4.0 [INFO] [stderr] Compiling clap v2.32.0 [INFO] [stderr] Compiling rust-htslib v0.22.1-alpha.0 (https://github.com/rust-bio/rust-htslib.git?rev=6a93aa473077c08aa52be0c2a89f1ee9d1c27609#6a93aa47) [INFO] [stderr] error: failed to run custom build command for `rust-htslib v0.22.1-alpha.0 (https://github.com/rust-bio/rust-htslib.git?rev=6a93aa473077c08aa52be0c2a89f1ee9d1c27609#6a93aa47)` [INFO] [stderr] note: To improve backtraces for build dependencies, set the CARGO_PROFILE_DEV_BUILD_OVERRIDE_DEBUG=true environment variable to enable debug information generation. [INFO] [stderr] [INFO] [stderr] Caused by: [INFO] [stderr] process didn't exit successfully: `/opt/rustwide/target/debug/build/rust-htslib-471f0ba57dea894c/build-script-build` (exit status: 101) [INFO] [stderr] --- stdout [INFO] [stderr] OPT_LEVEL = Some("0") [INFO] [stderr] TARGET = Some("x86_64-unknown-linux-gnu") [INFO] [stderr] HOST = Some("x86_64-unknown-linux-gnu") [INFO] [stderr] CC_x86_64-unknown-linux-gnu = None [INFO] [stderr] CC_x86_64_unknown_linux_gnu = None [INFO] [stderr] HOST_CC = None [INFO] [stderr] CC = None [INFO] [stderr] CFLAGS_x86_64-unknown-linux-gnu = None [INFO] [stderr] CFLAGS_x86_64_unknown_linux_gnu = None [INFO] [stderr] HOST_CFLAGS = None [INFO] [stderr] CFLAGS = None [INFO] [stderr] CRATE_CC_NO_DEFAULTS = None [INFO] [stderr] DEBUG = Some("true") [INFO] [stderr] echo '/* Default config.h generated by Makefile */' > config.h [INFO] [stderr] echo '#define HAVE_LIBBZ2 1' >> config.h [INFO] [stderr] echo '#define HAVE_LIBLZMA 1' >> config.h [INFO] [stderr] echo '#define HAVE_LZMA_H 1' >> config.h [INFO] [stderr] echo '#define HAVE_FSEEKO 1' >> config.h [INFO] [stderr] echo '#define HAVE_DRAND48 1' >> config.h [INFO] [stderr] cc -ffunction-sections -fdata-sections -fPIC -g -fno-omit-frame-pointer -m64 -static -I /opt/rustwide/target/debug/build/bzip2-sys-42847c40ddfebb29/out/include -I. -c -o kfunc.o kfunc.c [INFO] [stderr] cc -ffunction-sections -fdata-sections -fPIC -g -fno-omit-frame-pointer -m64 -static -I /opt/rustwide/target/debug/build/bzip2-sys-42847c40ddfebb29/out/include -I. -c -o knetfile.o knetfile.c [INFO] [stderr] cc -ffunction-sections -fdata-sections -fPIC -g -fno-omit-frame-pointer -m64 -static -I /opt/rustwide/target/debug/build/bzip2-sys-42847c40ddfebb29/out/include -I. -c -o kstring.o kstring.c [INFO] [stderr] cc -ffunction-sections -fdata-sections -fPIC -g -fno-omit-frame-pointer -m64 -static -I /opt/rustwide/target/debug/build/bzip2-sys-42847c40ddfebb29/out/include -I. -c -o bcf_sr_sort.o bcf_sr_sort.c [INFO] [stderr] cc -ffunction-sections -fdata-sections -fPIC -g -fno-omit-frame-pointer -m64 -static -I /opt/rustwide/target/debug/build/bzip2-sys-42847c40ddfebb29/out/include -I. -c -o bgzf.o bgzf.c [INFO] [stderr] cc -ffunction-sections -fdata-sections -fPIC -g -fno-omit-frame-pointer -m64 -static -I /opt/rustwide/target/debug/build/bzip2-sys-42847c40ddfebb29/out/include -I. -c -o errmod.o errmod.c [INFO] [stderr] cc -ffunction-sections -fdata-sections -fPIC -g -fno-omit-frame-pointer -m64 -static -I /opt/rustwide/target/debug/build/bzip2-sys-42847c40ddfebb29/out/include -I. -c -o faidx.o faidx.c [INFO] [stderr] cc -ffunction-sections -fdata-sections -fPIC -g -fno-omit-frame-pointer -m64 -static -I /opt/rustwide/target/debug/build/bzip2-sys-42847c40ddfebb29/out/include -I. -c -o hfile.o hfile.c [INFO] [stderr] cc -ffunction-sections -fdata-sections -fPIC -g -fno-omit-frame-pointer -m64 -static -I /opt/rustwide/target/debug/build/bzip2-sys-42847c40ddfebb29/out/include -I. -c -o hfile_net.o hfile_net.c [INFO] [stderr] echo '#define HTS_VERSION ""' > version.h [INFO] [stderr] cc -ffunction-sections -fdata-sections -fPIC -g -fno-omit-frame-pointer -m64 -static -I /opt/rustwide/target/debug/build/bzip2-sys-42847c40ddfebb29/out/include -I. -c -o hts.o hts.c [INFO] [stderr] cc -ffunction-sections -fdata-sections -fPIC -g -fno-omit-frame-pointer -m64 -static -I /opt/rustwide/target/debug/build/bzip2-sys-42847c40ddfebb29/out/include -I. -c -o hts_os.o hts_os.c [INFO] [stderr] cc -ffunction-sections -fdata-sections -fPIC -g -fno-omit-frame-pointer -m64 -static -I /opt/rustwide/target/debug/build/bzip2-sys-42847c40ddfebb29/out/include -I. -c -o md5.o md5.c [INFO] [stderr] cc -ffunction-sections -fdata-sections -fPIC -g -fno-omit-frame-pointer -m64 -static -I /opt/rustwide/target/debug/build/bzip2-sys-42847c40ddfebb29/out/include -I. -c -o multipart.o multipart.c [INFO] [stderr] cc -ffunction-sections -fdata-sections -fPIC -g -fno-omit-frame-pointer -m64 -static -I /opt/rustwide/target/debug/build/bzip2-sys-42847c40ddfebb29/out/include -I. -c -o probaln.o probaln.c [INFO] [stderr] cc -ffunction-sections -fdata-sections -fPIC -g -fno-omit-frame-pointer -m64 -static -I /opt/rustwide/target/debug/build/bzip2-sys-42847c40ddfebb29/out/include -I. -c -o realn.o realn.c [INFO] [stderr] cc -ffunction-sections -fdata-sections -fPIC -g -fno-omit-frame-pointer -m64 -static -I /opt/rustwide/target/debug/build/bzip2-sys-42847c40ddfebb29/out/include -I. -c -o regidx.o regidx.c [INFO] [stderr] cc -ffunction-sections -fdata-sections -fPIC -g -fno-omit-frame-pointer -m64 -static -I /opt/rustwide/target/debug/build/bzip2-sys-42847c40ddfebb29/out/include -I. -c -o sam.o sam.c [INFO] [stderr] cc -ffunction-sections -fdata-sections -fPIC -g -fno-omit-frame-pointer -m64 -static -I /opt/rustwide/target/debug/build/bzip2-sys-42847c40ddfebb29/out/include -I. -c -o synced_bcf_reader.o synced_bcf_reader.c [INFO] [stderr] cc -ffunction-sections -fdata-sections -fPIC -g -fno-omit-frame-pointer -m64 -static -I /opt/rustwide/target/debug/build/bzip2-sys-42847c40ddfebb29/out/include -I. -c -o vcf_sweep.o vcf_sweep.c [INFO] [stderr] cc -ffunction-sections -fdata-sections -fPIC -g -fno-omit-frame-pointer -m64 -static -I /opt/rustwide/target/debug/build/bzip2-sys-42847c40ddfebb29/out/include -I. -c -o tbx.o tbx.c [INFO] [stderr] cc -ffunction-sections -fdata-sections -fPIC -g -fno-omit-frame-pointer -m64 -static -I /opt/rustwide/target/debug/build/bzip2-sys-42847c40ddfebb29/out/include -I. -c -o textutils.o textutils.c [INFO] [stderr] cc -ffunction-sections -fdata-sections -fPIC -g -fno-omit-frame-pointer -m64 -static -I /opt/rustwide/target/debug/build/bzip2-sys-42847c40ddfebb29/out/include -I. -c -o thread_pool.o thread_pool.c [INFO] [stderr] cc -ffunction-sections -fdata-sections -fPIC -g -fno-omit-frame-pointer -m64 -static -I /opt/rustwide/target/debug/build/bzip2-sys-42847c40ddfebb29/out/include -I. -c -o vcf.o vcf.c [INFO] [stderr] cc -ffunction-sections -fdata-sections -fPIC -g -fno-omit-frame-pointer -m64 -static -I /opt/rustwide/target/debug/build/bzip2-sys-42847c40ddfebb29/out/include -I. -c -o vcfutils.o vcfutils.c [INFO] [stderr] cc -ffunction-sections -fdata-sections -fPIC -g -fno-omit-frame-pointer -m64 -static -I /opt/rustwide/target/debug/build/bzip2-sys-42847c40ddfebb29/out/include -I. -c -o cram/cram_codecs.o cram/cram_codecs.c [INFO] [stderr] cc -ffunction-sections -fdata-sections -fPIC -g -fno-omit-frame-pointer -m64 -static -I /opt/rustwide/target/debug/build/bzip2-sys-42847c40ddfebb29/out/include -I. -c -o cram/cram_decode.o cram/cram_decode.c [INFO] [stderr] cc -ffunction-sections -fdata-sections -fPIC -g -fno-omit-frame-pointer -m64 -static -I /opt/rustwide/target/debug/build/bzip2-sys-42847c40ddfebb29/out/include -I. -c -o cram/cram_encode.o cram/cram_encode.c [INFO] [stderr] cc -ffunction-sections -fdata-sections -fPIC -g -fno-omit-frame-pointer -m64 -static -I /opt/rustwide/target/debug/build/bzip2-sys-42847c40ddfebb29/out/include -I. -c -o cram/cram_external.o cram/cram_external.c [INFO] [stderr] cc -ffunction-sections -fdata-sections -fPIC -g -fno-omit-frame-pointer -m64 -static -I /opt/rustwide/target/debug/build/bzip2-sys-42847c40ddfebb29/out/include -I. -c -o cram/cram_index.o cram/cram_index.c [INFO] [stderr] cc -ffunction-sections -fdata-sections -fPIC -g -fno-omit-frame-pointer -m64 -static -I /opt/rustwide/target/debug/build/bzip2-sys-42847c40ddfebb29/out/include -I. -c -o cram/cram_io.o cram/cram_io.c [INFO] [stderr] cc -ffunction-sections -fdata-sections -fPIC -g -fno-omit-frame-pointer -m64 -static -I /opt/rustwide/target/debug/build/bzip2-sys-42847c40ddfebb29/out/include -I. -c -o cram/cram_samtools.o cram/cram_samtools.c [INFO] [stderr] cc -ffunction-sections -fdata-sections -fPIC -g -fno-omit-frame-pointer -m64 -static -I /opt/rustwide/target/debug/build/bzip2-sys-42847c40ddfebb29/out/include -I. -c -o cram/cram_stats.o cram/cram_stats.c [INFO] [stderr] cc -ffunction-sections -fdata-sections -fPIC -g -fno-omit-frame-pointer -m64 -static -I /opt/rustwide/target/debug/build/bzip2-sys-42847c40ddfebb29/out/include -I. -c -o cram/files.o cram/files.c [INFO] [stderr] cc -ffunction-sections -fdata-sections -fPIC -g -fno-omit-frame-pointer -m64 -static -I /opt/rustwide/target/debug/build/bzip2-sys-42847c40ddfebb29/out/include -I. -c -o cram/mFILE.o cram/mFILE.c [INFO] [stderr] cc -ffunction-sections -fdata-sections -fPIC -g -fno-omit-frame-pointer -m64 -static -I /opt/rustwide/target/debug/build/bzip2-sys-42847c40ddfebb29/out/include -I. -c -o cram/open_trace_file.o cram/open_trace_file.c [INFO] [stderr] cc -ffunction-sections -fdata-sections -fPIC -g -fno-omit-frame-pointer -m64 -static -I /opt/rustwide/target/debug/build/bzip2-sys-42847c40ddfebb29/out/include -I. -c -o cram/pooled_alloc.o cram/pooled_alloc.c [INFO] [stderr] cc -ffunction-sections -fdata-sections -fPIC -g -fno-omit-frame-pointer -m64 -static -I /opt/rustwide/target/debug/build/bzip2-sys-42847c40ddfebb29/out/include -I. -c -o cram/rANS_static.o cram/rANS_static.c [INFO] [stderr] cc -ffunction-sections -fdata-sections -fPIC -g -fno-omit-frame-pointer -m64 -static -I /opt/rustwide/target/debug/build/bzip2-sys-42847c40ddfebb29/out/include -I. -c -o cram/sam_header.o cram/sam_header.c [INFO] [stderr] cc -ffunction-sections -fdata-sections -fPIC -g -fno-omit-frame-pointer -m64 -static -I /opt/rustwide/target/debug/build/bzip2-sys-42847c40ddfebb29/out/include -I. -c -o cram/string_alloc.o cram/string_alloc.c [INFO] [stderr] ar -rc libhts.a kfunc.o knetfile.o kstring.o bcf_sr_sort.o bgzf.o errmod.o faidx.o hfile.o hfile_net.o hts.o hts_os.o md5.o multipart.o probaln.o realn.o regidx.o sam.o synced_bcf_reader.o vcf_sweep.o tbx.o textutils.o thread_pool.o vcf.o vcfutils.o cram/cram_codecs.o cram/cram_decode.o cram/cram_encode.o cram/cram_external.o cram/cram_index.o cram/cram_io.o cram/cram_samtools.o cram/cram_stats.o cram/files.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/rANS_static.o cram/sam_header.o cram/string_alloc.o [INFO] [stderr] ranlib libhts.a [INFO] [stderr] running: "cc" "-O0" "-ffunction-sections" "-fdata-sections" "-fPIC" "-g" "-fno-omit-frame-pointer" "-m64" "-static" "-I" "/opt/rustwide/target/debug/build/bzip2-sys-42847c40ddfebb29/out/include" "-o" "/opt/rustwide/target/debug/build/rust-htslib-f8305e0fa72bf46d/out/wrapper.o" "-c" "wrapper.c" [INFO] [stderr] exit status: 0 [INFO] [stderr] AR_x86_64-unknown-linux-gnu = None [INFO] [stderr] AR_x86_64_unknown_linux_gnu = None [INFO] [stderr] HOST_AR = None [INFO] [stderr] AR = None [INFO] [stderr] running: "ar" "crs" "/opt/rustwide/target/debug/build/rust-htslib-f8305e0fa72bf46d/out/libwrapper.a" "/opt/rustwide/target/debug/build/rust-htslib-f8305e0fa72bf46d/out/wrapper.o" [INFO] [stderr] exit status: 0 [INFO] [stderr] cargo:rustc-link-lib=static=wrapper [INFO] [stderr] cargo:rustc-link-search=native=/opt/rustwide/target/debug/build/rust-htslib-f8305e0fa72bf46d/out [INFO] [stderr] [INFO] [stderr] --- stderr [INFO] [stderr] fatal: No names found, cannot describe anything. [INFO] [stderr] fatal: No names found, cannot describe anything. [INFO] [stderr] hts.c: In function 'hts_idx_init': [INFO] [stderr] hts.c:1386:59: warning: overflow in conversion from 'uint32_t' {aka 'unsigned int'} to 'int' changes value from 'idx->z.last_bin = 4294967295' to '-1' [-Woverflow] [INFO] [stderr] 1386 | idx->z.save_bin = idx->z.save_tid = idx->z.last_tid = idx->z.last_bin = 0xffffffffu; [INFO] [stderr] | ^~~ [INFO] [stderr] [INFO] [stderr] thread 'main' panicked at /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/proc-macro2-0.4.29/src/fallback.rs:594:9: [INFO] [stderr] "htsFormat_struct_(unnamed_at__/htslib/htslib/hts_h_154_5)" is not a valid Ident [INFO] [stderr] stack backtrace: [INFO] [stderr] 0: 0x5d79ca8e0452 - std::backtrace_rs::backtrace::libunwind::trace::hd39b1f53d3cf9745 [INFO] [stderr] at /rustc/d98a5da813da67eb189387b8ccfb73cf481275d8/library/std/src/../../backtrace/src/backtrace/libunwind.rs:117:9 [INFO] [stderr] 1: 0x5d79ca8e0452 - std::backtrace_rs::backtrace::trace_unsynchronized::he91d9a75d4e3972b [INFO] [stderr] at /rustc/d98a5da813da67eb189387b8ccfb73cf481275d8/library/std/src/../../backtrace/src/backtrace/mod.rs:66:14 [INFO] [stderr] 2: 0x5d79ca8e0452 - std::sys::backtrace::_print_fmt::hca46938f8c6e22cf [INFO] [stderr] at /rustc/d98a5da813da67eb189387b8ccfb73cf481275d8/library/std/src/sys/backtrace.rs:66:9 [INFO] [stderr] 3: 0x5d79ca8e0452 - ::fmt::ha499add612cccf8e [INFO] [stderr] at /rustc/d98a5da813da67eb189387b8ccfb73cf481275d8/library/std/src/sys/backtrace.rs:39:26 [INFO] [stderr] 4: 0x5d79ca908fa3 - core::fmt::rt::Argument::fmt::hd21145b75a833b7a [INFO] [stderr] at /rustc/d98a5da813da67eb189387b8ccfb73cf481275d8/library/core/src/fmt/rt.rs:173:76 [INFO] [stderr] 5: 0x5d79ca908fa3 - core::fmt::write::hb10c956f5235c8a4 [INFO] [stderr] at /rustc/d98a5da813da67eb189387b8ccfb73cf481275d8/library/core/src/fmt/mod.rs:1465:25 [INFO] [stderr] 6: 0x5d79ca8dc9c3 - std::io::default_write_fmt::h1470b6bb31d733fd [INFO] [stderr] at /rustc/d98a5da813da67eb189387b8ccfb73cf481275d8/library/std/src/io/mod.rs:639:11 [INFO] [stderr] 7: 0x5d79ca8dc9c3 - std::io::Write::write_fmt::hd8146ab3991543d1 [INFO] [stderr] at /rustc/d98a5da813da67eb189387b8ccfb73cf481275d8/library/std/src/io/mod.rs:1954:13 [INFO] [stderr] 8: 0x5d79ca8e02a2 - std::sys::backtrace::BacktraceLock::print::hb47c770ef659fd10 [INFO] [stderr] at /rustc/d98a5da813da67eb189387b8ccfb73cf481275d8/library/std/src/sys/backtrace.rs:42:9 [INFO] [stderr] 9: 0x5d79ca8e24ec - std::panicking::default_hook::{{closure}}::hdda8afb9d457a22c [INFO] [stderr] at /rustc/d98a5da813da67eb189387b8ccfb73cf481275d8/library/std/src/panicking.rs:300:27 [INFO] [stderr] 10: 0x5d79ca8e22ef - std::panicking::default_hook::h7c46b44874fe5c9a [INFO] [stderr] at /rustc/d98a5da813da67eb189387b8ccfb73cf481275d8/library/std/src/panicking.rs:327:9 [INFO] [stderr] 11: 0x5d79ca8e2fcb - as core::ops::function::Fn>::call::h13602080f5b63276 [INFO] [stderr] at /rustc/d98a5da813da67eb189387b8ccfb73cf481275d8/library/alloc/src/boxed.rs:1985:9 [INFO] [stderr] 12: 0x5d79ca8e2fcb - std::panicking::rust_panic_with_hook::ha6cb99ed099eb1c5 [INFO] [stderr] at /rustc/d98a5da813da67eb189387b8ccfb73cf481275d8/library/std/src/panicking.rs:841:13 [INFO] [stderr] 13: 0x5d79ca8e2c9a - std::panicking::begin_panic_handler::{{closure}}::he11808bc797ee921 [INFO] [stderr] at /rustc/d98a5da813da67eb189387b8ccfb73cf481275d8/library/std/src/panicking.rs:706:13 [INFO] [stderr] 14: 0x5d79ca8e0959 - std::sys::backtrace::__rust_end_short_backtrace::h9418807cb7346258 [INFO] [stderr] at /rustc/d98a5da813da67eb189387b8ccfb73cf481275d8/library/std/src/sys/backtrace.rs:168:18 [INFO] [stderr] 15: 0x5d79ca8e292d - __rustc[18fb429eef004894]::rust_begin_unwind [INFO] [stderr] at /rustc/d98a5da813da67eb189387b8ccfb73cf481275d8/library/std/src/panicking.rs:697:5 [INFO] [stderr] 16: 0x5d79ca907420 - core::panicking::panic_fmt::hd890aeb12c3a3fc3 [INFO] [stderr] at /rustc/d98a5da813da67eb189387b8ccfb73cf481275d8/library/core/src/panicking.rs:75:14 [INFO] [stderr] 17: 0x5d79ca868998 - proc_macro2::fallback::Ident::_new::hdba71c8e7504231b [INFO] [stderr] 18: 0x5d79ca86fc3e - proc_macro2::Ident::new::h1c839294279d766d [INFO] [stderr] 19: 0x5d79ca7549c3 - bindgen::ir::context::BindgenContext::rust_ident::h041c4a736630c573 [INFO] [stderr] 20: 0x5d79ca7745af - ::codegen::hc34eae8d788c82cd [INFO] [stderr] 21: 0x5d79ca7d3d99 - ::codegen::hb965d6db8443719a [INFO] [stderr] 22: 0x5d79ca78af49 - ::codegen::h4f970c86412cff95 [INFO] [stderr] 23: 0x5d79ca777ecc - ::codegen::hc34eae8d788c82cd [INFO] [stderr] 24: 0x5d79ca7d3d99 - ::codegen::hb965d6db8443719a [INFO] [stderr] 25: 0x5d79ca78af49 - ::codegen::h4f970c86412cff95 [INFO] [stderr] 26: 0x5d79ca7a85cb - ::codegen::{{closure}}::h47e9a0c7db0fd108 [INFO] [stderr] 27: 0x5d79ca7a6e8d - ::codegen::hb73895ab058628c2 [INFO] [stderr] 28: 0x5d79ca78aeff - ::codegen::h4f970c86412cff95 [INFO] [stderr] 29: 0x5d79ca758402 - bindgen::ir::context::BindgenContext::gen::h4381e2f5e5e80a57 [INFO] [stderr] 30: 0x5d79ca73ef1e - bindgen::Builder::generate::h01fdc7e2073c17a4 [INFO] [stderr] 31: 0x5d79ca71befd - build_script_build::main::h37904ef385e90ab0 [INFO] [stderr] 32: 0x5d79ca71d243 - std::sys::backtrace::__rust_begin_short_backtrace::hb4bf591d0623d0fb [INFO] [stderr] 33: 0x5d79ca71d239 - std::rt::lang_start::{{closure}}::hf08385ab69853017 [INFO] [stderr] 34: 0x5d79ca8d7ae0 - core::ops::function::impls:: for &F>::call_once::h106557a9d245eb10 [INFO] [stderr] at /rustc/d98a5da813da67eb189387b8ccfb73cf481275d8/library/core/src/ops/function.rs:284:21 [INFO] [stderr] 35: 0x5d79ca8d7ae0 - std::panicking::catch_unwind::do_call::h18100d9574045a86 [INFO] [stderr] at /rustc/d98a5da813da67eb189387b8ccfb73cf481275d8/library/std/src/panicking.rs:589:40 [INFO] [stderr] 36: 0x5d79ca8d7ae0 - std::panicking::catch_unwind::hf9f86a2471d520c7 [INFO] [stderr] at /rustc/d98a5da813da67eb189387b8ccfb73cf481275d8/library/std/src/panicking.rs:552:19 [INFO] [stderr] 37: 0x5d79ca8d7ae0 - std::panic::catch_unwind::h410688ae8e8348a9 [INFO] [stderr] at /rustc/d98a5da813da67eb189387b8ccfb73cf481275d8/library/std/src/panic.rs:359:14 [INFO] [stderr] 38: 0x5d79ca8d7ae0 - std::rt::lang_start_internal::{{closure}}::h42fee7344f1a80c6 [INFO] [stderr] at /rustc/d98a5da813da67eb189387b8ccfb73cf481275d8/library/std/src/rt.rs:175:24 [INFO] [stderr] 39: 0x5d79ca8d7ae0 - std::panicking::catch_unwind::do_call::h62b4ab9c433ebcfb [INFO] [stderr] at /rustc/d98a5da813da67eb189387b8ccfb73cf481275d8/library/std/src/panicking.rs:589:40 [INFO] [stderr] 40: 0x5d79ca8d7ae0 - std::panicking::catch_unwind::h61ceb8228d4a4310 [INFO] [stderr] at /rustc/d98a5da813da67eb189387b8ccfb73cf481275d8/library/std/src/panicking.rs:552:19 [INFO] [stderr] 41: 0x5d79ca8d7ae0 - std::panic::catch_unwind::hf4a60a68b20bb306 [INFO] [stderr] at /rustc/d98a5da813da67eb189387b8ccfb73cf481275d8/library/std/src/panic.rs:359:14 [INFO] [stderr] 42: 0x5d79ca8d7ae0 - std::rt::lang_start_internal::h3478bd2aa4cc9cb2 [INFO] [stderr] at /rustc/d98a5da813da67eb189387b8ccfb73cf481275d8/library/std/src/rt.rs:171:5 [INFO] [stderr] 43: 0x5d79ca71d025 - main [INFO] [stderr] 44: 0x7e049a8471ca - [INFO] [stderr] 45: 0x7e049a84728b - __libc_start_main [INFO] [stderr] 46: 0x5d79ca718b65 - _start [INFO] [stderr] 47: 0x0 - [INFO] running `Command { std: "docker" "inspect" "5a3706d4848c59c9b495a19f8306719ee37bbf078b9696d4948d56e1901e0245", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "5a3706d4848c59c9b495a19f8306719ee37bbf078b9696d4948d56e1901e0245", kill_on_drop: false }` [INFO] [stdout] 5a3706d4848c59c9b495a19f8306719ee37bbf078b9696d4948d56e1901e0245