[INFO] cloning repository https://github.com/0ncorhynchus/pdbstat
[INFO] running `Command { std: "git" "-c" "credential.helper=" "-c" "credential.helper=/workspace/cargo-home/bin/git-credential-null" "clone" "--bare" "https://github.com/0ncorhynchus/pdbstat" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2F0ncorhynchus%2Fpdbstat", kill_on_drop: false }`
[INFO] [stderr] Cloning into bare repository '/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2F0ncorhynchus%2Fpdbstat'...
[INFO] running `Command { std: "git" "rev-parse" "HEAD", kill_on_drop: false }`
[INFO] [stdout] 4ad97d115b0b9b3e9628155b646db596a5063109
[INFO] checking 0ncorhynchus/pdbstat against 1.55.0 for beta-1.56-3
[INFO] running `Command { std: "git" "clone" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2F0ncorhynchus%2Fpdbstat" "/workspace/builds/worker-39/source", kill_on_drop: false }`
[INFO] [stderr] Cloning into '/workspace/builds/worker-39/source'...
[INFO] [stderr] done.
[INFO] validating manifest of git repo https://github.com/0ncorhynchus/pdbstat on toolchain 1.55.0
[INFO] running `Command { std: "/workspace/cargo-home/bin/cargo" "+1.55.0" "metadata" "--manifest-path" "Cargo.toml" "--no-deps", kill_on_drop: false }`
[INFO] started tweaking git repo https://github.com/0ncorhynchus/pdbstat
[INFO] finished tweaking git repo https://github.com/0ncorhynchus/pdbstat
[INFO] tweaked toml for git repo https://github.com/0ncorhynchus/pdbstat written to /workspace/builds/worker-39/source/Cargo.toml
[INFO] crate git repo https://github.com/0ncorhynchus/pdbstat already has a lockfile, it will not be regenerated
[INFO] running `Command { std: "/workspace/cargo-home/bin/cargo" "+1.55.0" "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] [stderr]  Downloading crates ...
[INFO] [stderr]   Downloaded cmake v0.1.24
[INFO] [stderr]   Downloaded libc v0.2.24
[INFO] [stderr]   Downloaded chemfiles v0.7.40
[INFO] [stderr]   Downloaded chemfiles-sys v0.7.40
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-39/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-39/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:a89201d6b5b9fd45c15d5952ece0a0129e7e80cb26ec023fd59cf09bc26f1604" "/opt/rustwide/cargo-home/bin/cargo" "+1.55.0" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }`
[INFO] [stdout] 582097cbc92aef6d3585b3c2fee2c26f267b67cb0e5e648c17c08a7597368000
[INFO] running `Command { std: "docker" "start" "-a" "582097cbc92aef6d3585b3c2fee2c26f267b67cb0e5e648c17c08a7597368000", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "inspect" "582097cbc92aef6d3585b3c2fee2c26f267b67cb0e5e648c17c08a7597368000", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "582097cbc92aef6d3585b3c2fee2c26f267b67cb0e5e648c17c08a7597368000", kill_on_drop: false }`
[INFO] [stdout] 582097cbc92aef6d3585b3c2fee2c26f267b67cb0e5e648c17c08a7597368000
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-39/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-39/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=warn" "-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:a89201d6b5b9fd45c15d5952ece0a0129e7e80cb26ec023fd59cf09bc26f1604" "/opt/rustwide/cargo-home/bin/cargo" "+1.55.0" "check" "--frozen" "--all" "--all-targets" "--message-format=json", kill_on_drop: false }`
[INFO] [stdout] 54e43570b563fc3576c7e89e3a555c2fd007b6ed1f94477a48a82f72cc4d32a8
[INFO] running `Command { std: "docker" "start" "-a" "54e43570b563fc3576c7e89e3a555c2fd007b6ed1f94477a48a82f72cc4d32a8", kill_on_drop: false }`
[INFO] [stderr]     Blocking waiting for file lock on package cache
[INFO] [stderr]    Compiling gcc v0.3.51
[INFO] [stderr]     Checking libc v0.2.24
[INFO] [stderr]    Compiling cmake v0.1.24
[INFO] [stderr]    Compiling chemfiles-sys v0.7.40
[INFO] [stderr] error: failed to run custom build command for `chemfiles-sys v0.7.40`
[INFO] [stderr] 
[INFO] [stderr] Caused by:
[INFO] [stderr]   process didn't exit successfully: `/opt/rustwide/target/debug/build/chemfiles-sys-6f053f14ec9866ba/build-script-build` (exit status: 101)
[INFO] [stderr]   --- stdout
[INFO] [stderr]   running: "cmake" "/opt/rustwide/cargo-home/registry/src/github.com-1ecc6299db9ec823/chemfiles-sys-0.7.40/." "-DBUILD_SHARED_LIBS=OFF" "-DCMAKE_POSITION_INDEPENDENT_CODE=ON" "-DCMAKE_INSTALL_PREFIX=/opt/rustwide/target/debug/build/chemfiles-sys-f5449be26e20a803/out" "-DCMAKE_C_FLAGS= -ffunction-sections -fdata-sections -fPIC -m64" "-DCMAKE_C_COMPILER=/usr/bin/cc" "-DCMAKE_CXX_FLAGS= -ffunction-sections -fdata-sections -fPIC -m64" "-DCMAKE_CXX_COMPILER=/usr/bin/c++" "-DCMAKE_BUILD_TYPE=Debug"
[INFO] [stderr]   -- The C compiler identification is GNU 9.3.0
[INFO] [stderr]   -- The CXX compiler identification is GNU 9.3.0
[INFO] [stderr]   -- Check for working C compiler: /usr/bin/cc
[INFO] [stderr]   -- Check for working C compiler: /usr/bin/cc -- works
[INFO] [stderr]   -- Detecting C compiler ABI info
[INFO] [stderr]   -- Detecting C compiler ABI info - done
[INFO] [stderr]   -- Detecting C compile features
[INFO] [stderr]   -- Detecting C compile features - done
[INFO] [stderr]   -- Check for working CXX compiler: /usr/bin/c++
[INFO] [stderr]   -- Check for working CXX compiler: /usr/bin/c++ -- works
[INFO] [stderr]   -- Detecting CXX compiler ABI info
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[INFO] [stderr]   -- Detecting CXX compile features
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[INFO] [stderr]   -- Unpacking fmt sources
[INFO] [stderr]   -- Unpacking netcdf sources
[INFO] [stderr]   -- Unpacking tng sources
[INFO] [stderr]   -- Check if the system is big endian
[INFO] [stderr]   -- Searching 16 bit integer
[INFO] [stderr]   -- Using unsigned short
[INFO] [stderr]   -- Check if the system is big endian - little endian
[INFO] [stderr]   -- Unpacking molfiles sources
[INFO] [stderr]   -- Configuring done
[INFO] [stderr]   -- Generating done
[INFO] [stderr]   -- Build files have been written to: /opt/rustwide/target/debug/build/chemfiles-sys-f5449be26e20a803/out/build
[INFO] [stderr]   running: "cmake" "--build" "." "--target" "install" "--config" "Debug" "--" "-j128"
[INFO] [stderr]   Scanning dependencies of target fmt
[INFO] [stderr]   Scanning dependencies of target chemfiles_files
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[INFO] [stderr]     CMake is pretending there is a "project(Project)" command on the first
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[INFO] [stderr]   This warning is for project developers.  Use -Wno-dev to suppress it.
[INFO] [stderr] 
[INFO] [stderr]   CMake Deprecation Warning at chemfiles/CMakeLists.txt:8 (cmake_policy):
[INFO] [stderr]     The OLD behavior for policy CMP0042 will be removed from a future version
[INFO] [stderr]     of CMake.
[INFO] [stderr] 
[INFO] [stderr]     The cmake-policies(7) manual explains that the OLD behaviors of all
[INFO] [stderr]     policies are deprecated and that a policy should be set to OLD only under
[INFO] [stderr]     specific short-term circumstances.  Projects should be ported to the NEW
[INFO] [stderr]     behavior and not rely on setting a policy to OLD.
[INFO] [stderr] 
[INFO] [stderr] 
[INFO] [stderr]   c++: fatal error: Killed signal terminated program cc1plus
[INFO] [stderr]   compilation terminated.
[INFO] [stderr]   make[2]: *** [chemfiles/CMakeFiles/chemfiles.dir/build.make:284: chemfiles/CMakeFiles/chemfiles.dir/src/capi/topology.cpp.o] Error 1
[INFO] [stderr]   make[2]: *** Waiting for unfinished jobs....
[INFO] [stderr]   c++: fatal error: Killed signal terminated program cc1plus
[INFO] [stderr]   compilation terminated.
[INFO] [stderr]   make[2]: *** [chemfiles/CMakeFiles/chemfiles.dir/build.make:323: chemfiles/CMakeFiles/chemfiles.dir/src/formats/NcFormat.cpp.o] Error 1
[INFO] [stderr]   c++: fatal error: Killed signal terminated program cc1plus
[INFO] [stderr]   compilation terminated.
[INFO] [stderr]   make[2]: *** [chemfiles/CMakeFiles/chemfiles.dir/build.make:310: chemfiles/CMakeFiles/chemfiles.dir/src/formats/Molfile.cpp.o] Error 1
[INFO] [stderr]   make[1]: *** [CMakeFiles/Makefile2:252: chemfiles/CMakeFiles/chemfiles.dir/all] Error 2
[INFO] [stderr]   make: *** [Makefile:130: all] Error 2
[INFO] [stderr]   thread 'main' panicked at '
[INFO] [stderr]   command did not execute successfully, got: exit status: 2
[INFO] [stderr] 
[INFO] [stderr]   build script failed, must exit now', /opt/rustwide/cargo-home/registry/src/github.com-1ecc6299db9ec823/cmake-0.1.24/src/lib.rs:593:5
[INFO] [stderr]   stack backtrace:
[INFO] [stderr]      0:     0x55beb6d72200 - std::backtrace_rs::backtrace::libunwind::trace::ha0ad43e8a952bfe7
[INFO] [stderr]                                  at /rustc/c8dfcfe046a7680554bf4eb612bad840e7631c4b/library/std/src/../../backtrace/src/backtrace/libunwind.rs:90:5
[INFO] [stderr]      1:     0x55beb6d72200 - std::backtrace_rs::backtrace::trace_unsynchronized::h6830419c0c4130dc
[INFO] [stderr]                                  at /rustc/c8dfcfe046a7680554bf4eb612bad840e7631c4b/library/std/src/../../backtrace/src/backtrace/mod.rs:66:5
[INFO] [stderr]      2:     0x55beb6d72200 - std::sys_common::backtrace::_print_fmt::h8f3516631ffa1ef5
[INFO] [stderr]                                  at /rustc/c8dfcfe046a7680554bf4eb612bad840e7631c4b/library/std/src/sys_common/backtrace.rs:67:5
[INFO] [stderr]      3:     0x55beb6d72200 - <std::sys_common::backtrace::_print::DisplayBacktrace as core::fmt::Display>::fmt::he1640d5f0d93f618
[INFO] [stderr]                                  at /rustc/c8dfcfe046a7680554bf4eb612bad840e7631c4b/library/std/src/sys_common/backtrace.rs:46:22
[INFO] [stderr]      4:     0x55beb6d912ac - core::fmt::write::h88012e1f01caeebf
[INFO] [stderr]                                  at /rustc/c8dfcfe046a7680554bf4eb612bad840e7631c4b/library/core/src/fmt/mod.rs:1115:17
[INFO] [stderr]      5:     0x55beb6d6f455 - std::io::Write::write_fmt::h360fa85b30182555
[INFO] [stderr]                                  at /rustc/c8dfcfe046a7680554bf4eb612bad840e7631c4b/library/std/src/io/mod.rs:1665:15
[INFO] [stderr]      6:     0x55beb6d744cb - std::sys_common::backtrace::_print::ha1f00492f406a015
[INFO] [stderr]                                  at /rustc/c8dfcfe046a7680554bf4eb612bad840e7631c4b/library/std/src/sys_common/backtrace.rs:49:5
[INFO] [stderr]      7:     0x55beb6d744cb - std::sys_common::backtrace::print::hd54561b13feb6af3
[INFO] [stderr]                                  at /rustc/c8dfcfe046a7680554bf4eb612bad840e7631c4b/library/std/src/sys_common/backtrace.rs:36:9
[INFO] [stderr]      8:     0x55beb6d744cb - std::panicking::default_hook::{{closure}}::h84fe124cd0864662
[INFO] [stderr]                                  at /rustc/c8dfcfe046a7680554bf4eb612bad840e7631c4b/library/std/src/panicking.rs:208:50
[INFO] [stderr]      9:     0x55beb6d73fa1 - std::panicking::default_hook::h5a8e74a76ce290a7
[INFO] [stderr]                                  at /rustc/c8dfcfe046a7680554bf4eb612bad840e7631c4b/library/std/src/panicking.rs:225:9
[INFO] [stderr]     10:     0x55beb6d74b94 - std::panicking::rust_panic_with_hook::h67c812a4fe9d4c91
[INFO] [stderr]                                  at /rustc/c8dfcfe046a7680554bf4eb612bad840e7631c4b/library/std/src/panicking.rs:622:17
[INFO] [stderr]     11:     0x55beb6d74677 - std::panicking::begin_panic_handler::{{closure}}::h33f9c1b96af300d7
[INFO] [stderr]                                  at /rustc/c8dfcfe046a7680554bf4eb612bad840e7631c4b/library/std/src/panicking.rs:519:13
[INFO] [stderr]     12:     0x55beb6d726fc - std::sys_common::backtrace::__rust_end_short_backtrace::h51bae64be5921f0e
[INFO] [stderr]                                  at /rustc/c8dfcfe046a7680554bf4eb612bad840e7631c4b/library/std/src/sys_common/backtrace.rs:141:18
[INFO] [stderr]     13:     0x55beb6d745d9 - rust_begin_unwind
[INFO] [stderr]                                  at /rustc/c8dfcfe046a7680554bf4eb612bad840e7631c4b/library/std/src/panicking.rs:515:5
[INFO] [stderr]     14:     0x55beb6d26bbb - std::panicking::begin_panic_fmt::h7ab3d84aa4ae32a2
[INFO] [stderr]                                  at /rustc/c8dfcfe046a7680554bf4eb612bad840e7631c4b/library/std/src/panicking.rs:457:5
[INFO] [stderr]     15:     0x55beb6d30773 - cmake::fail::h017fa1fb2d2288c4
[INFO] [stderr]                                  at /opt/rustwide/cargo-home/registry/src/github.com-1ecc6299db9ec823/cmake-0.1.24/src/lib.rs:593:5
[INFO] [stderr]     16:     0x55beb6d30181 - cmake::run::hdfa0885be2bd394b
[INFO] [stderr]                                  at /opt/rustwide/cargo-home/registry/src/github.com-1ecc6299db9ec823/cmake-0.1.24/src/lib.rs:574:9
[INFO] [stderr]     17:     0x55beb6d2dc55 - cmake::Config::build::h3206419542255ef5
[INFO] [stderr]                                  at /opt/rustwide/cargo-home/registry/src/github.com-1ecc6299db9ec823/cmake-0.1.24/src/lib.rs:481:9
[INFO] [stderr]     18:     0x55beb6d29083 - build_script_build::main::hab79006c6a917957
[INFO] [stderr]                                  at /opt/rustwide/cargo-home/registry/src/github.com-1ecc6299db9ec823/chemfiles-sys-0.7.40/build.rs:19:15
[INFO] [stderr]     19:     0x55beb6d28bfb - core::ops::function::FnOnce::call_once::h7287c63d32603378
[INFO] [stderr]                                  at /rustc/c8dfcfe046a7680554bf4eb612bad840e7631c4b/library/core/src/ops/function.rs:227:5
[INFO] [stderr]     20:     0x55beb6d2ae6e - std::sys_common::backtrace::__rust_begin_short_backtrace::hb0ac27abde36f762
[INFO] [stderr]                                  at /rustc/c8dfcfe046a7680554bf4eb612bad840e7631c4b/library/std/src/sys_common/backtrace.rs:125:18
[INFO] [stderr]     21:     0x55beb6d28a81 - std::rt::lang_start::{{closure}}::h14b09c5ec3876b1d
[INFO] [stderr]                                  at /rustc/c8dfcfe046a7680554bf4eb612bad840e7631c4b/library/std/src/rt.rs:63:18
[INFO] [stderr]     22:     0x55beb6d7509a - core::ops::function::impls::<impl core::ops::function::FnOnce<A> for &F>::call_once::ha9408abe89f69dc4
[INFO] [stderr]                                  at /rustc/c8dfcfe046a7680554bf4eb612bad840e7631c4b/library/core/src/ops/function.rs:259:13
[INFO] [stderr]     23:     0x55beb6d7509a - std::panicking::try::do_call::h5b0cc9e9102acb65
[INFO] [stderr]                                  at /rustc/c8dfcfe046a7680554bf4eb612bad840e7631c4b/library/std/src/panicking.rs:401:40
[INFO] [stderr]     24:     0x55beb6d7509a - std::panicking::try::hddc7f8229138b3ba
[INFO] [stderr]                                  at /rustc/c8dfcfe046a7680554bf4eb612bad840e7631c4b/library/std/src/panicking.rs:365:19
[INFO] [stderr]     25:     0x55beb6d7509a - std::panic::catch_unwind::hfa401ff8bab2986e
[INFO] [stderr]                                  at /rustc/c8dfcfe046a7680554bf4eb612bad840e7631c4b/library/std/src/panic.rs:434:14
[INFO] [stderr]     26:     0x55beb6d7509a - std::rt::lang_start_internal::{{closure}}::h8163422320d11405
[INFO] [stderr]                                  at /rustc/c8dfcfe046a7680554bf4eb612bad840e7631c4b/library/std/src/rt.rs:45:48
[INFO] [stderr]     27:     0x55beb6d7509a - std::panicking::try::do_call::hc742cc7bb4f0fb20
[INFO] [stderr]                                  at /rustc/c8dfcfe046a7680554bf4eb612bad840e7631c4b/library/std/src/panicking.rs:401:40
[INFO] [stderr]     28:     0x55beb6d7509a - std::panicking::try::ha37d8d2dd1acf7d3
[INFO] [stderr]                                  at /rustc/c8dfcfe046a7680554bf4eb612bad840e7631c4b/library/std/src/panicking.rs:365:19
[INFO] [stderr]     29:     0x55beb6d7509a - std::panic::catch_unwind::h8a5381d5ecf437bc
[INFO] [stderr]                                  at /rustc/c8dfcfe046a7680554bf4eb612bad840e7631c4b/library/std/src/panic.rs:434:14
[INFO] [stderr]     30:     0x55beb6d7509a - std::rt::lang_start_internal::h7e2cee8c90d4a4d3
[INFO] [stderr]                                  at /rustc/c8dfcfe046a7680554bf4eb612bad840e7631c4b/library/std/src/rt.rs:45:20
[INFO] [stderr]     31:     0x55beb6d28a50 - std::rt::lang_start::h1a79b927e562384e
[INFO] [stderr]                                  at /rustc/c8dfcfe046a7680554bf4eb612bad840e7631c4b/library/std/src/rt.rs:62:5
[INFO] [stderr]     32:     0x55beb6d29c5c - main
[INFO] [stderr]     33:     0x7f87392e80b3 - __libc_start_main
[INFO] [stderr]     34:     0x55beb6d2795e - _start
[INFO] [stderr]     35:                0x0 - <unknown>
[INFO] running `Command { std: "docker" "inspect" "54e43570b563fc3576c7e89e3a555c2fd007b6ed1f94477a48a82f72cc4d32a8", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "54e43570b563fc3576c7e89e3a555c2fd007b6ed1f94477a48a82f72cc4d32a8", kill_on_drop: false }`
[INFO] [stdout] 54e43570b563fc3576c7e89e3a555c2fd007b6ed1f94477a48a82f72cc4d32a8
