[INFO] cloning repository https://github.com/swemeshy/counts_to_csv [INFO] running `Command { std: "git" "-c" "credential.helper=" "-c" "credential.helper=/workspace/cargo-home/bin/git-credential-null" "clone" "--bare" "https://github.com/swemeshy/counts_to_csv" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fswemeshy%2Fcounts_to_csv", kill_on_drop: false }` [INFO] [stderr] Cloning into bare repository '/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fswemeshy%2Fcounts_to_csv'... [INFO] running `Command { std: "git" "rev-parse" "HEAD", kill_on_drop: false }` [INFO] [stdout] 416d6b6a25b07251ddbe10a79b9b16a97b0d73c7 [INFO] checking swemeshy/counts_to_csv against master#33fdb797f59421c7bbecaa4588ed5d7a31a9494a for pr-87190-3 [INFO] running `Command { std: "git" "clone" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fswemeshy%2Fcounts_to_csv" "/workspace/builds/worker-18/source", kill_on_drop: false }` [INFO] [stderr] Cloning into '/workspace/builds/worker-18/source'... [INFO] [stderr] done. [INFO] validating manifest of git repo https://github.com/swemeshy/counts_to_csv on toolchain 33fdb797f59421c7bbecaa4588ed5d7a31a9494a [INFO] running `Command { std: "/workspace/cargo-home/bin/cargo" "+33fdb797f59421c7bbecaa4588ed5d7a31a9494a" "metadata" "--manifest-path" "Cargo.toml" "--no-deps", kill_on_drop: false }` [INFO] started tweaking git repo https://github.com/swemeshy/counts_to_csv [INFO] finished tweaking git repo https://github.com/swemeshy/counts_to_csv [INFO] tweaked toml for git repo https://github.com/swemeshy/counts_to_csv written to /workspace/builds/worker-18/source/Cargo.toml [INFO] crate git repo https://github.com/swemeshy/counts_to_csv already has a lockfile, it will not be regenerated [INFO] running `Command { std: "/workspace/cargo-home/bin/cargo" "+33fdb797f59421c7bbecaa4588ed5d7a31a9494a" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }` [INFO] [stderr] Blocking waiting for file lock on package cache [INFO] [stderr] Blocking waiting for file lock on package cache [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-18/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-18/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@sha256:34b6a614d2c27851fe6cbf88fbd1137609cefab8b10d0615aaeb6fd47975d74e" "/opt/rustwide/cargo-home/bin/cargo" "+33fdb797f59421c7bbecaa4588ed5d7a31a9494a" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }` [INFO] [stdout] 1fa1f05ab3c836ed962535d84c6c73193a73561c648d34d27ed4666bb78a1500 [INFO] running `Command { std: "docker" "start" "-a" "1fa1f05ab3c836ed962535d84c6c73193a73561c648d34d27ed4666bb78a1500", kill_on_drop: false }` [INFO] running `Command { std: "docker" "inspect" "1fa1f05ab3c836ed962535d84c6c73193a73561c648d34d27ed4666bb78a1500", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "1fa1f05ab3c836ed962535d84c6c73193a73561c648d34d27ed4666bb78a1500", kill_on_drop: false }` [INFO] [stdout] 1fa1f05ab3c836ed962535d84c6c73193a73561c648d34d27ed4666bb78a1500 [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-18/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-18/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" "-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@sha256:34b6a614d2c27851fe6cbf88fbd1137609cefab8b10d0615aaeb6fd47975d74e" "/opt/rustwide/cargo-home/bin/cargo" "+33fdb797f59421c7bbecaa4588ed5d7a31a9494a" "check" "--frozen" "--all" "--all-targets" "--message-format=json", kill_on_drop: false }` [INFO] [stdout] d168a134d3bc4c505311c2f85b24c499d8b2cba85b3c241d03422f41bc745db9 [INFO] running `Command { std: "docker" "start" "-a" "d168a134d3bc4c505311c2f85b24c499d8b2cba85b3c241d03422f41bc745db9", kill_on_drop: false }` [INFO] [stderr] Blocking waiting for file lock on package cache [INFO] [stderr] Compiling proc-macro2 v1.0.24 [INFO] [stderr] Compiling unicode-xid v0.2.1 [INFO] [stderr] Compiling libc v0.2.88 [INFO] [stderr] Compiling syn v1.0.67 [INFO] [stderr] Compiling memchr v2.3.4 [INFO] [stderr] Compiling libm v0.2.1 [INFO] [stderr] Compiling cfg-if v1.0.0 [INFO] [stderr] Compiling regex-syntax v0.6.23 [INFO] [stderr] Checking rawpointer v0.2.1 [INFO] [stderr] Compiling rayon-core v1.9.0 [INFO] [stderr] Compiling serde_derive v1.0.124 [INFO] [stderr] Checking smallvec v1.6.1 [INFO] [stderr] Compiling serde v1.0.124 [INFO] [stderr] Checking unicode-width v0.1.8 [INFO] [stderr] Compiling unicode-segmentation v1.7.1 [INFO] [stderr] Checking byteorder v1.4.3 [INFO] [stderr] Compiling unindent v0.1.7 [INFO] [stderr] Compiling inventory v0.1.10 [INFO] [stderr] Compiling ndarray v0.13.1 [INFO] [stderr] Compiling log v0.4.14 [INFO] [stderr] Compiling hdf5-types v0.7.1 (https://github.com/aldanor/hdf5-rust.git?rev=24beeaa914a05c67adc78f0c161925fd4627d407#24beeaa9) [INFO] [stderr] Compiling pyo3 v0.13.2 [INFO] [stderr] Checking hashbrown v0.9.1 [INFO] [stderr] Checking either v1.6.1 [INFO] [stderr] Compiling hdf5 v0.7.1 (https://github.com/aldanor/hdf5-rust.git?rev=24beeaa914a05c67adc78f0c161925fd4627d407#24beeaa9) [INFO] [stderr] Compiling anyhow v1.0.38 [INFO] [stderr] Checking ascii v1.0.0 [INFO] [stderr] Checking termcolor v1.1.2 [INFO] [stderr] Checking number_prefix v0.3.0 [INFO] [stderr] Checking strsim v0.10.0 [INFO] [stderr] Checking vec_map v0.8.2 [INFO] [stderr] Checking os_str_bytes v2.4.0 [INFO] [stderr] Compiling num-traits v0.2.14 [INFO] [stderr] Compiling crossbeam-utils v0.8.3 [INFO] [stderr] Compiling num-integer v0.1.44 [INFO] [stderr] Compiling memoffset v0.6.1 [INFO] [stderr] Compiling num-complex v0.2.4 [INFO] [stderr] Compiling indexmap v1.6.2 [INFO] [stderr] Compiling rayon v1.5.0 [INFO] [stderr] Compiling proc-macro-hack v0.5.19 [INFO] [stderr] Compiling proc-macro-error-attr v1.0.4 [INFO] [stderr] Compiling proc-macro-error v1.0.4 [INFO] [stderr] Checking instant v0.1.9 [INFO] [stderr] Checking lock_api v0.4.2 [INFO] [stderr] Compiling ryu v1.0.5 [INFO] [stderr] Compiling libloading v0.7.0 [INFO] [stderr] Checking matrixmultiply v0.2.4 [INFO] [stderr] Checking matrixmultiply v0.3.1 [INFO] [stderr] Checking regex-automata v0.1.9 [INFO] [stderr] Checking textwrap v0.12.1 [INFO] [stderr] Compiling heck v0.3.2 [INFO] [stderr] Compiling aho-corasick v0.7.15 [INFO] [stderr] Checking atty v0.2.14 [INFO] [stderr] Checking num_cpus v1.13.0 [INFO] [stderr] Checking parking_lot_core v0.8.3 [INFO] [stderr] Checking time v0.1.44 [INFO] [stderr] Checking terminal_size v0.1.16 [INFO] [stderr] Compiling paste-impl v0.1.18 [INFO] [stderr] Checking csv-core v0.1.10 [INFO] [stderr] Compiling quote v1.0.9 [INFO] [stderr] Checking colored v1.9.3 [INFO] [stderr] Checking parking_lot v0.11.1 [INFO] [stderr] Checking paste v0.1.18 [INFO] [stderr] Checking regex v1.4.4 [INFO] [stderr] Checking crossbeam-epoch v0.9.3 [INFO] [stderr] Checking crossbeam-channel v0.5.0 [INFO] [stderr] Checking approx v0.3.2 [INFO] [stderr] Checking num-complex v0.4.0 [INFO] [stderr] Checking console v0.14.1 [INFO] [stderr] Checking crossbeam-deque v0.8.0 [INFO] [stderr] Checking chrono v0.4.19 [INFO] [stderr] Checking ndarray v0.15.3 [INFO] [stderr] Checking indicatif v0.15.0 [INFO] [stderr] Checking alga v0.9.3 [INFO] [stderr] Checking simple_logger v1.11.0 [INFO] [stderr] Compiling hdf5-sys v0.7.1 (https://github.com/aldanor/hdf5-rust.git?rev=24beeaa914a05c67adc78f0c161925fd4627d407#24beeaa9) [INFO] [stderr] Compiling pyo3-macros-backend v0.13.2 [INFO] [stderr] error: failed to run custom build command for `hdf5-sys v0.7.1 (https://github.com/aldanor/hdf5-rust.git?rev=24beeaa914a05c67adc78f0c161925fd4627d407#24beeaa9)` [INFO] [stderr] [INFO] [stderr] Caused by: [INFO] [stderr] process didn't exit successfully: `/opt/rustwide/target/debug/build/hdf5-sys-f55201341888becd/build-script-build` (exit status: 101) [INFO] [stderr] --- stdout [INFO] [stderr] Attempting to find HDF5 via pkg-config... [INFO] [stderr] cargo:rerun-if-env-changed=HDF5_NO_PKG_CONFIG [INFO] [stderr] cargo:rerun-if-env-changed=PKG_CONFIG [INFO] [stderr] cargo:rerun-if-env-changed=HDF5_STATIC [INFO] [stderr] cargo:rerun-if-env-changed=HDF5_DYNAMIC [INFO] [stderr] cargo:rerun-if-env-changed=PKG_CONFIG_ALL_STATIC [INFO] [stderr] cargo:rerun-if-env-changed=PKG_CONFIG_ALL_DYNAMIC [INFO] [stderr] cargo:rerun-if-env-changed=PKG_CONFIG_PATH_x86_64-unknown-linux-gnu [INFO] [stderr] cargo:rerun-if-env-changed=PKG_CONFIG_PATH_x86_64_unknown_linux_gnu [INFO] [stderr] cargo:rerun-if-env-changed=HOST_PKG_CONFIG_PATH [INFO] [stderr] cargo:rerun-if-env-changed=PKG_CONFIG_PATH [INFO] [stderr] cargo:rerun-if-env-changed=PKG_CONFIG_LIBDIR_x86_64-unknown-linux-gnu [INFO] [stderr] cargo:rerun-if-env-changed=PKG_CONFIG_LIBDIR_x86_64_unknown_linux_gnu [INFO] [stderr] cargo:rerun-if-env-changed=HOST_PKG_CONFIG_LIBDIR [INFO] [stderr] cargo:rerun-if-env-changed=PKG_CONFIG_LIBDIR [INFO] [stderr] cargo:rerun-if-env-changed=PKG_CONFIG_SYSROOT_DIR_x86_64-unknown-linux-gnu [INFO] [stderr] cargo:rerun-if-env-changed=PKG_CONFIG_SYSROOT_DIR_x86_64_unknown_linux_gnu [INFO] [stderr] cargo:rerun-if-env-changed=HOST_PKG_CONFIG_SYSROOT_DIR [INFO] [stderr] cargo:rerun-if-env-changed=PKG_CONFIG_SYSROOT_DIR [INFO] [stderr] [INFO] [stderr] --- stderr [INFO] [stderr] thread 'main' panicked at 'Unable to locate HDF5 root directory and/or headers.', /opt/rustwide/cargo-home/git/checkouts/hdf5-rust-c1072d7a2617f7d8/24beeaa/hdf5-sys/build.rs:547:13 [INFO] [stderr] stack backtrace: [INFO] [stderr] 0: 0x556a032a6a6c - std::backtrace_rs::backtrace::libunwind::trace::ha21b6ba3016b6364 [INFO] [stderr] at /rustc/33fdb797f59421c7bbecaa4588ed5d7a31a9494a/library/std/src/../../backtrace/src/backtrace/libunwind.rs:90:5 [INFO] [stderr] 1: 0x556a032a6a6c - std::backtrace_rs::backtrace::trace_unsynchronized::hf515241a118c4e5a [INFO] [stderr] at /rustc/33fdb797f59421c7bbecaa4588ed5d7a31a9494a/library/std/src/../../backtrace/src/backtrace/mod.rs:66:5 [INFO] [stderr] 2: 0x556a032a6a6c - std::sys_common::backtrace::_print_fmt::h339cd474d88b8467 [INFO] [stderr] at /rustc/33fdb797f59421c7bbecaa4588ed5d7a31a9494a/library/std/src/sys_common/backtrace.rs:67:5 [INFO] [stderr] 3: 0x556a032a6a6c - ::fmt::h06b8f714a0700be1 [INFO] [stderr] at /rustc/33fdb797f59421c7bbecaa4588ed5d7a31a9494a/library/std/src/sys_common/backtrace.rs:46:22 [INFO] [stderr] 4: 0x556a032c447c - core::fmt::write::h9a6d9c74526a6c1b [INFO] [stderr] at /rustc/33fdb797f59421c7bbecaa4588ed5d7a31a9494a/library/core/src/fmt/mod.rs:1117:17 [INFO] [stderr] 5: 0x556a032a3d35 - std::io::Write::write_fmt::hb1c61d571fcd8cbf [INFO] [stderr] at /rustc/33fdb797f59421c7bbecaa4588ed5d7a31a9494a/library/std/src/io/mod.rs:1667:15 [INFO] [stderr] 6: 0x556a032a84c0 - std::sys_common::backtrace::_print::hcd1fe1237ea0c752 [INFO] [stderr] at /rustc/33fdb797f59421c7bbecaa4588ed5d7a31a9494a/library/std/src/sys_common/backtrace.rs:49:5 [INFO] [stderr] 7: 0x556a032a84c0 - std::sys_common::backtrace::print::hae7d6625a78cd32e [INFO] [stderr] at /rustc/33fdb797f59421c7bbecaa4588ed5d7a31a9494a/library/std/src/sys_common/backtrace.rs:36:9 [INFO] [stderr] 8: 0x556a032a84c0 - std::panicking::default_hook::{{closure}}::h9a7fffa4e6b396ed [INFO] [stderr] at /rustc/33fdb797f59421c7bbecaa4588ed5d7a31a9494a/library/std/src/panicking.rs:210:50 [INFO] [stderr] 9: 0x556a032a807b - std::panicking::default_hook::h5dc58e323cddd123 [INFO] [stderr] at /rustc/33fdb797f59421c7bbecaa4588ed5d7a31a9494a/library/std/src/panicking.rs:227:9 [INFO] [stderr] 10: 0x556a032a8b74 - std::panicking::rust_panic_with_hook::hbef17e4338d7de57 [INFO] [stderr] at /rustc/33fdb797f59421c7bbecaa4588ed5d7a31a9494a/library/std/src/panicking.rs:624:17 [INFO] [stderr] 11: 0x556a031e6db2 - std::panicking::begin_panic::{{closure}}::hd45b1c50f4a3b967 [INFO] [stderr] at /rustc/33fdb797f59421c7bbecaa4588ed5d7a31a9494a/library/std/src/panicking.rs:544:9 [INFO] [stderr] 12: 0x556a031d3669 - std::sys_common::backtrace::__rust_end_short_backtrace::h762999170a7ec46d [INFO] [stderr] at /rustc/33fdb797f59421c7bbecaa4588ed5d7a31a9494a/library/std/src/sys_common/backtrace.rs:141:18 [INFO] [stderr] 13: 0x556a031e6cf3 - std::panicking::begin_panic::h7fdfb821c4e1eaa2 [INFO] [stderr] at /rustc/33fdb797f59421c7bbecaa4588ed5d7a31a9494a/library/std/src/panicking.rs:543:12 [INFO] [stderr] 14: 0x556a030aab87 - build_script_build::LibrarySearcher::try_locate_hdf5_library::h55996b65dcaba399 [INFO] [stderr] at /opt/rustwide/cargo-home/git/checkouts/hdf5-rust-c1072d7a2617f7d8/24beeaa/hdf5-sys/build.rs:547:13 [INFO] [stderr] 15: 0x556a030ac357 - build_script_build::main::he52794673f2efa48 [INFO] [stderr] at /opt/rustwide/cargo-home/git/checkouts/hdf5-rust-c1072d7a2617f7d8/24beeaa/hdf5-sys/build.rs:645:9 [INFO] [stderr] 16: 0x556a030b94bb - core::ops::function::FnOnce::call_once::he701e00f3b455d5d [INFO] [stderr] at /rustc/33fdb797f59421c7bbecaa4588ed5d7a31a9494a/library/core/src/ops/function.rs:227:5 [INFO] [stderr] 17: 0x556a030b8fde - std::sys_common::backtrace::__rust_begin_short_backtrace::h292d44688272a486 [INFO] [stderr] at /rustc/33fdb797f59421c7bbecaa4588ed5d7a31a9494a/library/std/src/sys_common/backtrace.rs:125:18 [INFO] [stderr] 18: 0x556a030b75b1 - std::rt::lang_start::{{closure}}::h133a739e73999933 [INFO] [stderr] at /rustc/33fdb797f59421c7bbecaa4588ed5d7a31a9494a/library/std/src/rt.rs:63:18 [INFO] [stderr] 19: 0x556a032a907a - core::ops::function::impls:: for &F>::call_once::hc9bc8961e4809a14 [INFO] [stderr] at /rustc/33fdb797f59421c7bbecaa4588ed5d7a31a9494a/library/core/src/ops/function.rs:259:13 [INFO] [stderr] 20: 0x556a032a907a - std::panicking::try::do_call::h6f00e12df2af6579 [INFO] [stderr] at /rustc/33fdb797f59421c7bbecaa4588ed5d7a31a9494a/library/std/src/panicking.rs:403:40 [INFO] [stderr] 21: 0x556a032a907a - std::panicking::try::h588c31a0a9a8ad2c [INFO] [stderr] at /rustc/33fdb797f59421c7bbecaa4588ed5d7a31a9494a/library/std/src/panicking.rs:367:19 [INFO] [stderr] 22: 0x556a032a907a - std::panic::catch_unwind::h8ebc4fcb0e51bec0 [INFO] [stderr] at /rustc/33fdb797f59421c7bbecaa4588ed5d7a31a9494a/library/std/src/panic.rs:129:14 [INFO] [stderr] 23: 0x556a032a907a - std::rt::lang_start_internal::{{closure}}::had93e50fbfd893a1 [INFO] [stderr] at /rustc/33fdb797f59421c7bbecaa4588ed5d7a31a9494a/library/std/src/rt.rs:45:48 [INFO] [stderr] 24: 0x556a032a907a - std::panicking::try::do_call::hf70c5056d8b410b7 [INFO] [stderr] at /rustc/33fdb797f59421c7bbecaa4588ed5d7a31a9494a/library/std/src/panicking.rs:403:40 [INFO] [stderr] 25: 0x556a032a907a - std::panicking::try::h0c680320de5deb84 [INFO] [stderr] at /rustc/33fdb797f59421c7bbecaa4588ed5d7a31a9494a/library/std/src/panicking.rs:367:19 [INFO] [stderr] 26: 0x556a032a907a - std::panic::catch_unwind::h7b94a99f13366c53 [INFO] [stderr] at /rustc/33fdb797f59421c7bbecaa4588ed5d7a31a9494a/library/std/src/panic.rs:129:14 [INFO] [stderr] 27: 0x556a032a907a - std::rt::lang_start_internal::hca14fb2549072049 [INFO] [stderr] at /rustc/33fdb797f59421c7bbecaa4588ed5d7a31a9494a/library/std/src/rt.rs:45:20 [INFO] [stderr] 28: 0x556a030b7580 - std::rt::lang_start::h1db90fb30eb6b4ba [INFO] [stderr] at /rustc/33fdb797f59421c7bbecaa4588ed5d7a31a9494a/library/std/src/rt.rs:62:5 [INFO] [stderr] 29: 0x556a030ad80c - main [INFO] [stderr] 30: 0x7f45948f40b3 - __libc_start_main [INFO] [stderr] 31: 0x556a030a5ede - _start [INFO] [stderr] 32: 0x0 - [INFO] [stderr] warning: build failed, waiting for other jobs to finish... [INFO] [stderr] error: build failed [INFO] running `Command { std: "docker" "inspect" "d168a134d3bc4c505311c2f85b24c499d8b2cba85b3c241d03422f41bc745db9", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "d168a134d3bc4c505311c2f85b24c499d8b2cba85b3c241d03422f41bc745db9", kill_on_drop: false }` [INFO] [stdout] d168a134d3bc4c505311c2f85b24c499d8b2cba85b3c241d03422f41bc745db9