[INFO] fetching crate openbabel 0.5.4... [INFO] testing openbabel-0.5.4 against master#c90bcb9571b7aab0d8beaa2ce8a998ffaf079d38 for pr-146098-8 [INFO] extracting crate openbabel 0.5.4 into /workspace/builds/worker-1-tc1/source [INFO] started tweaking crates.io crate openbabel 0.5.4 [INFO] removed 0 missing examples [INFO] finished tweaking crates.io crate openbabel 0.5.4 [INFO] tweaked toml for crates.io crate openbabel 0.5.4 written to /workspace/builds/worker-1-tc1/source/Cargo.toml [INFO] validating manifest of crates.io crate openbabel 0.5.4 on toolchain c90bcb9571b7aab0d8beaa2ce8a998ffaf079d38 [INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+c90bcb9571b7aab0d8beaa2ce8a998ffaf079d38" "metadata" "--manifest-path" "Cargo.toml" "--no-deps", kill_on_drop: false }` [INFO] crate crates.io crate openbabel 0.5.4 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" "+c90bcb9571b7aab0d8beaa2ce8a998ffaf079d38" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }` [INFO] [stderr] Updating crates.io index [INFO] [stderr] Blocking waiting for file lock on package cache [INFO] [stderr] Downloading crates ... [INFO] [stderr] Downloaded link-cplusplus v1.0.6 [INFO] [stderr] Downloaded fs_extra v1.2.0 [INFO] [stderr] Downloaded scratch v1.0.1 [INFO] [stderr] Downloaded serde_derive v1.0.137 [INFO] [stderr] Downloaded chiral-db-sources v0.2.0 [INFO] [stderr] Downloaded cxxbridge-flags v1.0.67 [INFO] [stderr] Downloaded clap v4.5.26 [INFO] [stderr] Downloaded cxx-build v1.0.68 [INFO] [stderr] Downloaded rayon-core v1.9.3 [INFO] [stderr] Downloaded cxxbridge-macro v1.0.67 [INFO] [stderr] Downloaded serde_json v1.0.81 [INFO] [stderr] Downloaded rayon v1.5.3 [INFO] [stderr] Downloaded serde v1.0.137 [INFO] [stderr] Downloaded cxx v1.0.67 [INFO] [stderr] Downloaded clap_builder v4.5.26 [INFO] [stderr] Downloaded regex v1.5.6 [INFO] [stderr] Downloaded regex-syntax v0.6.26 [INFO] [stderr] Downloaded openbabel-sys v0.5.4+openbabel-3.1.1 [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-1-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-1-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@sha256:4848fb76d95f26979359cc7e45710b1dbc8f3acb7aeedee7c460d7702230f228" "/opt/rustwide/cargo-home/bin/cargo" "+c90bcb9571b7aab0d8beaa2ce8a998ffaf079d38" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }` [INFO] [stdout] d3388e9f19a9f38f0209df5fd1cea3340b97020ce1389b9db2200e15c3a648ea [INFO] running `Command { std: "docker" "start" "-a" "d3388e9f19a9f38f0209df5fd1cea3340b97020ce1389b9db2200e15c3a648ea", kill_on_drop: false }` [INFO] running `Command { std: "docker" "inspect" "d3388e9f19a9f38f0209df5fd1cea3340b97020ce1389b9db2200e15c3a648ea", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "d3388e9f19a9f38f0209df5fd1cea3340b97020ce1389b9db2200e15c3a648ea", kill_on_drop: false }` [INFO] [stdout] d3388e9f19a9f38f0209df5fd1cea3340b97020ce1389b9db2200e15c3a648ea [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-1-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-1-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" "-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@sha256:4848fb76d95f26979359cc7e45710b1dbc8f3acb7aeedee7c460d7702230f228" "/opt/rustwide/cargo-home/bin/cargo" "+c90bcb9571b7aab0d8beaa2ce8a998ffaf079d38" "build" "--frozen" "--message-format=json", kill_on_drop: false }` [INFO] [stdout] 206b6ac31f7c1ffcf9d9c7cd8c16d3b6bdeda4eea2a615c2b13f92899176db77 [INFO] running `Command { std: "docker" "start" "-a" "206b6ac31f7c1ffcf9d9c7cd8c16d3b6bdeda4eea2a615c2b13f92899176db77", kill_on_drop: false }` [INFO] [stderr] Compiling proc-macro2 v1.0.93 [INFO] [stderr] Compiling syn v1.0.91 [INFO] [stderr] Compiling scratch v1.0.1 [INFO] [stderr] Compiling cxxbridge-flags v1.0.67 [INFO] [stderr] Compiling termcolor v1.1.3 [INFO] [stderr] Compiling unicode-width v0.1.9 [INFO] [stderr] Compiling once_cell v1.20.2 [INFO] [stderr] Compiling rustversion v1.0.9 [INFO] [stderr] Compiling serde_derive v1.0.137 [INFO] [stderr] Compiling fs_extra v1.2.0 [INFO] [stderr] Compiling serde v1.0.137 [INFO] [stderr] Compiling link-cplusplus v1.0.6 [INFO] [stderr] Compiling cxx v1.0.67 [INFO] [stderr] Compiling codespan-reporting v0.11.1 [INFO] [stderr] Compiling quote v1.0.38 [INFO] [stderr] Compiling syn v2.0.96 [INFO] [stderr] Compiling strum_macros v0.26.4 [INFO] [stderr] Compiling cxx-build v1.0.68 [INFO] [stderr] Compiling cxxbridge-macro v1.0.67 [INFO] [stderr] Compiling strum v0.26.3 [INFO] [stderr] Compiling openbabel-sys v0.5.4+openbabel-3.1.1 [INFO] [stderr] Compiling openbabel v0.5.4 (/opt/rustwide/workdir) [INFO] [stdout] warning: struct `StringForMol` is never constructed [INFO] [stdout] --> src/io/mod.rs:8:8 [INFO] [stdout] | [INFO] [stdout] 8 | struct StringForMol { [INFO] [stdout] | ^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(dead_code)]` (part of `#[warn(unused)]`) on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: method `as_str` is never used [INFO] [stdout] --> src/io/mod.rs:14:12 [INFO] [stdout] | [INFO] [stdout] 13 | impl StringForMol { [INFO] [stdout] | ----------------- method in this implementation [INFO] [stdout] 14 | pub fn as_str(&self) -> &str { [INFO] [stdout] | ^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: struct `FileForMol` is never constructed [INFO] [stdout] --> src/io/mod.rs:37:8 [INFO] [stdout] | [INFO] [stdout] 37 | struct FileForMol<'a> { [INFO] [stdout] | ^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: enum `InputFormat` is never used [INFO] [stdout] --> src/io/formats.rs:12:10 [INFO] [stdout] | [INFO] [stdout] 12 | pub enum InputFormat { [INFO] [stdout] | ^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stderr] Finished `dev` profile [unoptimized + debuginfo] target(s) in 2m 25s [INFO] [stderr] warning: the following packages contain code that will be rejected by a future version of Rust: fs_extra v1.2.0 [INFO] [stderr] note: to see what the problems were, use the option `--future-incompat-report`, or run `cargo report future-incompatibilities --id 1` [INFO] running `Command { std: "docker" "inspect" "206b6ac31f7c1ffcf9d9c7cd8c16d3b6bdeda4eea2a615c2b13f92899176db77", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "206b6ac31f7c1ffcf9d9c7cd8c16d3b6bdeda4eea2a615c2b13f92899176db77", kill_on_drop: false }` [INFO] [stdout] 206b6ac31f7c1ffcf9d9c7cd8c16d3b6bdeda4eea2a615c2b13f92899176db77 [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-1-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-1-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" "-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@sha256:4848fb76d95f26979359cc7e45710b1dbc8f3acb7aeedee7c460d7702230f228" "/opt/rustwide/cargo-home/bin/cargo" "+c90bcb9571b7aab0d8beaa2ce8a998ffaf079d38" "test" "--frozen" "--no-run" "--message-format=json", kill_on_drop: false }` [INFO] [stdout] 1c16cc316ad7aeb3a826966bda17877d1e6ecf9b153fe56270f74f55fc4bbb12 [INFO] running `Command { std: "docker" "start" "-a" "1c16cc316ad7aeb3a826966bda17877d1e6ecf9b153fe56270f74f55fc4bbb12", kill_on_drop: false }` [INFO] [stderr] Compiling rayon-core v1.9.3 [INFO] [stderr] Compiling num-traits v0.2.15 [INFO] [stderr] Compiling either v1.6.1 [INFO] [stderr] Compiling serde_json v1.0.81 [INFO] [stderr] Compiling rayon v1.5.3 [INFO] [stderr] Compiling half v2.4.1 [INFO] [stderr] Compiling cxx-build v1.0.68 [INFO] [stderr] Compiling rand_core v0.6.3 [INFO] [stderr] Compiling plotters-backend v0.3.2 [INFO] [stderr] Compiling clap_builder v4.5.26 [INFO] [stderr] Compiling regex-syntax v0.6.26 [INFO] [stderr] Compiling is-terminal v0.4.13 [INFO] [stderr] Compiling walkdir v2.3.2 [INFO] [stderr] Compiling itertools v0.10.3 [INFO] [stderr] Compiling rand_chacha v0.3.1 [INFO] [stderr] Compiling plotters-svg v0.3.1 [INFO] [stderr] Compiling ciborium-ll v0.2.2 [INFO] [stderr] Compiling rand v0.8.5 [INFO] [stderr] Compiling ciborium v0.2.2 [INFO] [stderr] Compiling regex v1.5.6 [INFO] [stderr] Compiling plotters v0.3.1 [INFO] [stderr] Compiling chiral-db-sources v0.2.0 [INFO] [stderr] Compiling tinytemplate v1.2.1 [INFO] [stderr] Compiling criterion-plot v0.5.0 [INFO] [stderr] Compiling clap v4.5.26 [INFO] [stderr] Compiling openbabel-sys v0.5.4+openbabel-3.1.1 [INFO] [stderr] Compiling criterion v0.5.1 [INFO] [stderr] Compiling openbabel v0.5.4 (/opt/rustwide/workdir) [INFO] [stdout] warning: struct `StringForMol` is never constructed [INFO] [stdout] --> src/io/mod.rs:8:8 [INFO] [stdout] | [INFO] [stdout] 8 | struct StringForMol { [INFO] [stdout] | ^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(dead_code)]` (part of `#[warn(unused)]`) on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: method `as_str` is never used [INFO] [stdout] --> src/io/mod.rs:14:12 [INFO] [stdout] | [INFO] [stdout] 13 | impl StringForMol { [INFO] [stdout] | ----------------- method in this implementation [INFO] [stdout] 14 | pub fn as_str(&self) -> &str { [INFO] [stdout] | ^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: struct `FileForMol` is never constructed [INFO] [stdout] --> src/io/mod.rs:37:8 [INFO] [stdout] | [INFO] [stdout] 37 | struct FileForMol<'a> { [INFO] [stdout] | ^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: enum `InputFormat` is never used [INFO] [stdout] --> src/io/formats.rs:12:10 [INFO] [stdout] | [INFO] [stdout] 12 | pub enum InputFormat { [INFO] [stdout] | ^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stderr] Finished `test` profile [unoptimized + debuginfo] target(s) in 2m 26s [INFO] [stderr] warning: the following packages contain code that will be rejected by a future version of Rust: fs_extra v1.2.0 [INFO] [stderr] note: to see what the problems were, use the option `--future-incompat-report`, or run `cargo report future-incompatibilities --id 1` [INFO] running `Command { std: "docker" "inspect" "1c16cc316ad7aeb3a826966bda17877d1e6ecf9b153fe56270f74f55fc4bbb12", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "1c16cc316ad7aeb3a826966bda17877d1e6ecf9b153fe56270f74f55fc4bbb12", kill_on_drop: false }` [INFO] [stdout] 1c16cc316ad7aeb3a826966bda17877d1e6ecf9b153fe56270f74f55fc4bbb12 [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-1-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-1-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" "-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@sha256:4848fb76d95f26979359cc7e45710b1dbc8f3acb7aeedee7c460d7702230f228" "/opt/rustwide/cargo-home/bin/cargo" "+c90bcb9571b7aab0d8beaa2ce8a998ffaf079d38" "test" "--frozen", kill_on_drop: false }` [INFO] [stdout] 7cd75fcc7238792e660b9657f96525c67c535d2414f79ffa5ce9a5f3db0195ed [INFO] running `Command { std: "docker" "start" "-a" "7cd75fcc7238792e660b9657f96525c67c535d2414f79ffa5ce9a5f3db0195ed", kill_on_drop: false }` [INFO] [stderr] warning: struct `StringForMol` is never constructed [INFO] [stderr] --> src/io/mod.rs:8:8 [INFO] [stderr] | [INFO] [stderr] 8 | struct StringForMol { [INFO] [stderr] | ^^^^^^^^^^^^ [INFO] [stderr] | [INFO] [stdout] [INFO] [stderr] = note: `#[warn(dead_code)]` (part of `#[warn(unused)]`) on by default [INFO] [stdout] running 10 tests [INFO] [stderr] [INFO] [stdout] test fingerprint::test_mod_fingerprint::test_get_fp ... ok [INFO] [stderr] warning: method `as_str` is never used [INFO] [stderr] --> src/io/mod.rs:14:12 [INFO] [stderr] | [INFO] [stderr] 13 | impl StringForMol { [INFO] [stderr] | ----------------- method in this implementation [INFO] [stderr] 14 | pub fn as_str(&self) -> &str { [INFO] [stderr] | ^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: struct `FileForMol` is never constructed [INFO] [stderr] --> src/io/mod.rs:37:8 [INFO] [stderr] | [INFO] [stderr] 37 | struct FileForMol<'a> { [INFO] [stderr] | ^^^^^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: enum `InputFormat` is never used [INFO] [stderr] --> src/io/formats.rs:12:10 [INFO] [stderr] | [INFO] [stderr] 12 | pub enum InputFormat { [INFO] [stderr] | ^^^^^^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: `openbabel` (lib) generated 4 warnings [INFO] [stderr] Finished `test` profile [unoptimized + debuginfo] target(s) in 0.19s [INFO] [stderr] warning: the following packages contain code that will be rejected by a future version of Rust: fs_extra v1.2.0 [INFO] [stderr] note: to see what the problems were, use the option `--future-incompat-report`, or run `cargo report future-incompatibilities --id 1` [INFO] [stderr] Running unittests src/lib.rs (/opt/rustwide/target/debug/deps/openbabel-df912a63bfc82980) [INFO] [stderr] ============================== [INFO] [stderr] *** Open Babel Error in ReadFile [INFO] [stderr] Cannot read from ./openbabel-sys/openbabel/test/files/00T_ideal.pdb [INFO] [stderr] ============================== [INFO] [stderr] *** Open Babel Error in OBConversion_read_file [INFO] [stderr] OBConversion::ReadFile error [INFO] [stderr] [INFO] [stderr] ============================== [INFO] [stderr] *** Open Babel Error in ReadFile [INFO] [stderr] Cannot read from ./openbabel-sys/openbabel/test/files/3o8g_uff.sdf [INFO] [stderr] ============================== [INFO] [stderr] *** Open Babel Error in OBConversion_read_file [INFO] [stderr] OBConversion::ReadFile error [INFO] [stderr] [INFO] [stderr] ============================== [INFO] [stderr] *** Open Babel Error in ParseParamFile [INFO] [stderr] Cannot open gaff.dat [INFO] [stderr] ============================== [INFO] [stderr] *** Open Babel Error in ReadPatternFile [INFO] [stderr] Cannot open patterns.txt [INFO] [stderr] [INFO] [stderr] ============================== [INFO] [stderr] *** Open Babel Error in ReadPatternFile [INFO] [stderr] Cannot open SMARTS_InteLigand.txt [INFO] [stderr] [INFO] [stderr] ============================== [INFO] [stderr] *** Open Babel Error in SetTypes [INFO] [stderr] Cannot open gaff.prm [INFO] [stderr] ============================== [INFO] [stderr] *** Open Babel Error in OBForceField_setup [INFO] [stderr] OBForceField->Setup() error [INFO] [stderr] [INFO] [stderr] ============================== [INFO] [stderr] *** Open Babel Error in ParseParamFile [INFO] [stderr] Cannot open ghemical.prm [INFO] [stderr] ============================== [INFO] [stderr] *** Open Babel Error in SetTypes [INFO] [stderr] Cannot open ghemical.prm [INFO] [stderr] ============================== [INFO] [stderr] *** Open Babel Error in OBForceField_setup [INFO] [stderr] OBForceField->Setup() error [INFO] [stderr] [INFO] [stderr] munmap_chunk(): invalid pointer [INFO] [stderr] error: test failed, to rerun pass `--lib` [INFO] [stderr] [INFO] [stderr] Caused by: [INFO] [stderr] process didn't exit successfully: `/opt/rustwide/target/debug/deps/openbabel-df912a63bfc82980` (signal: 6, SIGABRT: process abort signal) [INFO] running `Command { std: "docker" "inspect" "7cd75fcc7238792e660b9657f96525c67c535d2414f79ffa5ce9a5f3db0195ed", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "7cd75fcc7238792e660b9657f96525c67c535d2414f79ffa5ce9a5f3db0195ed", kill_on_drop: false }` [INFO] [stdout] 7cd75fcc7238792e660b9657f96525c67c535d2414f79ffa5ce9a5f3db0195ed