[INFO] crate coverm 0.2.0-alpha6 is already in cache [INFO] extracting crate coverm 0.2.0-alpha6 into work/ex/pr-61874/sources/master#9f06855064ed06a50c496577b21ca50f92a2e67d/reg/coverm/0.2.0-alpha6 [INFO] extracting crate coverm 0.2.0-alpha6 into work/ex/pr-61874/sources/try#d3301713b54af69ca9de941a8c6b0d8287dbd6df/reg/coverm/0.2.0-alpha6 [INFO] validating manifest of coverm-0.2.0-alpha6 on toolchain master#9f06855064ed06a50c496577b21ca50f92a2e67d [INFO] running `"/mnt/big/crater/work/local/cargo-home/bin/cargo" "+9f06855064ed06a50c496577b21ca50f92a2e67d-alt" "read-manifest" "--manifest-path" "Cargo.toml"` [INFO] validating manifest of coverm-0.2.0-alpha6 on toolchain try#d3301713b54af69ca9de941a8c6b0d8287dbd6df [INFO] running `"/mnt/big/crater/work/local/cargo-home/bin/cargo" "+d3301713b54af69ca9de941a8c6b0d8287dbd6df-alt" "read-manifest" "--manifest-path" "Cargo.toml"` [INFO] started frobbing coverm-0.2.0-alpha6 [INFO] finished frobbing coverm-0.2.0-alpha6 [INFO] frobbed toml for coverm-0.2.0-alpha6 written to work/ex/pr-61874/sources/master#9f06855064ed06a50c496577b21ca50f92a2e67d/reg/coverm/0.2.0-alpha6/Cargo.toml [INFO] started frobbing coverm-0.2.0-alpha6 [INFO] finished frobbing coverm-0.2.0-alpha6 [INFO] frobbed toml for coverm-0.2.0-alpha6 written to work/ex/pr-61874/sources/try#d3301713b54af69ca9de941a8c6b0d8287dbd6df/reg/coverm/0.2.0-alpha6/Cargo.toml [INFO] running `"/mnt/big/crater/work/local/cargo-home/bin/cargo" "+9f06855064ed06a50c496577b21ca50f92a2e67d-alt" "generate-lockfile" "--manifest-path" "Cargo.toml" "-Zno-index-update"` [INFO] running `"/mnt/big/crater/work/local/cargo-home/bin/cargo" "+d3301713b54af69ca9de941a8c6b0d8287dbd6df-alt" "generate-lockfile" "--manifest-path" "Cargo.toml" "-Zno-index-update"` [INFO] running `"/mnt/big/crater/work/local/cargo-home/bin/cargo" "+9f06855064ed06a50c496577b21ca50f92a2e67d-alt" "fetch" "--locked" "--manifest-path" "Cargo.toml"` [INFO] running `"/mnt/big/crater/work/local/cargo-home/bin/cargo" "+d3301713b54af69ca9de941a8c6b0d8287dbd6df-alt" "fetch" "--locked" "--manifest-path" "Cargo.toml"` [INFO] checking coverm-0.2.0-alpha6 against try#d3301713b54af69ca9de941a8c6b0d8287dbd6df for pr-61874 [INFO] running `"docker" "create" "-v" "/mnt/big/crater/work/local/target-dirs/pr-61874/worker-0/try#d3301713b54af69ca9de941a8c6b0d8287dbd6df:/opt/crater/target:rw,Z" "-v" "/mnt/big/crater/work/ex/pr-61874/sources/try#d3301713b54af69ca9de941a8c6b0d8287dbd6df/reg/coverm/0.2.0-alpha6:/opt/crater/workdir:ro,Z" "-v" "/mnt/big/crater/work/local/cargo-home:/opt/crater/cargo-home:ro,Z" "-v" "/mnt/big/crater/work/local/rustup-home:/opt/crater/rustup-home:ro,Z" "-e" "USER_ID=1000" "-e" "SOURCE_DIR=/opt/crater/workdir" "-e" "MAP_USER_ID=1000" "-e" "CARGO_TARGET_DIR=/opt/crater/target" "-e" "CARGO_INCREMENTAL=0" "-e" "RUST_BACKTRACE=full" "-e" "RUSTFLAGS=--cap-lints=forbid" "-e" "CARGO_HOME=/opt/crater/cargo-home" "-e" "RUSTUP_HOME=/opt/crater/rustup-home" "-w" "/opt/crater/workdir" "-m" "1536M" "--network" "none" "rustops/crates-build-env" "/opt/crater/cargo-home/bin/cargo" "+d3301713b54af69ca9de941a8c6b0d8287dbd6df-alt" "check" "--frozen" "--all" "--all-targets"` [INFO] [stdout] d57721067321c230bae8e35041305f76fc139e2a0aa06af55ef973c5be6e5a61 [INFO] running `"docker" "start" "-a" "d57721067321c230bae8e35041305f76fc139e2a0aa06af55ef973c5be6e5a61"` [INFO] [stderr] Compiling bindgen v0.36.1 [INFO] [stderr] Compiling winapi v0.3.7 [INFO] [stderr] Checking linear-map v1.2.0 [INFO] [stderr] Compiling clang-sys v0.22.0 [INFO] [stderr] Compiling fs-utils v1.1.1 [INFO] [stderr] Compiling memchr v2.2.0 [INFO] [stderr] Checking nix v0.13.1 [INFO] [stderr] Compiling vec_map v0.8.1 [INFO] [stderr] Checking bv v0.10.0 [INFO] [stderr] Checking multimap v0.4.0 [INFO] [stderr] Checking bio-types v0.5.1 [INFO] [stderr] Compiling aho-corasick v0.7.3 [INFO] [stderr] Compiling aho-corasick v0.6.10 [INFO] [stderr] Compiling clap v2.33.0 [INFO] [stderr] Checking winconsole v0.10.0 [INFO] [stderr] Compiling regex v0.2.11 [INFO] [stderr] Compiling regex v1.1.7 [INFO] [stderr] Checking colored v1.8.0 [INFO] [stderr] Checking bio v0.25.0 [INFO] [stderr] Checking assert_cli v0.6.3 [INFO] [stderr] Compiling env_logger v0.5.13 [INFO] [stderr] Compiling rust-htslib v0.22.0 [INFO] [stderr] Checking coverm v0.2.0-alpha6 (/opt/crater/workdir) [INFO] [stderr] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stderr] --> src/bam_generator.rs:521:20 [INFO] [stderr] | [INFO] [stderr] 521 | pub index: Box, [INFO] [stderr] | ^^^^^^^^^^^^^^ help: use `dyn`: `dyn BwaIndexStruct` [INFO] [stderr] | [INFO] [stderr] = note: #[warn(bare_trait_objects)] on by default [INFO] [stderr] [INFO] [stderr] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stderr] --> src/coverage_takers.rs:6:31 [INFO] [stderr] | [INFO] [stderr] 6 | print_stream: &'a mut std::io::Write, [INFO] [stderr] | ^^^^^^^^^^^^^^ help: use `dyn`: `dyn std::io::Write` [INFO] [stderr] [INFO] [stderr] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stderr] --> src/coverage_takers.rs:10:31 [INFO] [stderr] | [INFO] [stderr] 10 | print_stream: &'a mut std::io::Write, [INFO] [stderr] | ^^^^^^^^^^^^^^ help: use `dyn`: `dyn std::io::Write` [INFO] [stderr] [INFO] [stderr] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stderr] --> src/coverage_takers.rs:46:28 [INFO] [stderr] | [INFO] [stderr] 46 | print_stream: &mut std::io::Write) -> CoverageTakerType { [INFO] [stderr] | ^^^^^^^^^^^^^^ help: use `dyn`: `dyn std::io::Write` [INFO] [stderr] [INFO] [stderr] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stderr] --> src/coverage_takers.rs:53:28 [INFO] [stderr] | [INFO] [stderr] 53 | print_stream: &mut std::io::Write) -> CoverageTakerType { [INFO] [stderr] | ^^^^^^^^^^^^^^ help: use `dyn`: `dyn std::io::Write` [INFO] [stderr] [INFO] [stderr] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stderr] --> src/coverage_printer.rs:20:28 [INFO] [stderr] | [INFO] [stderr] 20 | print_stream: &mut std::io::Write, [INFO] [stderr] | ^^^^^^^^^^^^^^ help: use `dyn`: `dyn std::io::Write` [INFO] [stderr] [INFO] [stderr] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stderr] --> src/coverage_printer.rs:97:28 [INFO] [stderr] | [INFO] [stderr] 97 | print_stream: &mut std::io::Write) { [INFO] [stderr] | ^^^^^^^^^^^^^^ help: use `dyn`: `dyn std::io::Write` [INFO] [stderr] [INFO] [stderr] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stderr] --> src/coverage_printer.rs:126:24 [INFO] [stderr] | [INFO] [stderr] 126 | print_stream: &mut std::io::Write, [INFO] [stderr] | ^^^^^^^^^^^^^^ help: use `dyn`: `dyn std::io::Write` [INFO] [stderr] [INFO] [stderr] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stderr] --> src/coverage_printer.rs:253:24 [INFO] [stderr] | [INFO] [stderr] 253 | print_stream: &mut std::io::Write, [INFO] [stderr] | ^^^^^^^^^^^^^^ help: use `dyn`: `dyn std::io::Write` [INFO] [stderr] [INFO] [stderr] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stderr] --> src/bam_generator.rs:521:20 [INFO] [stderr] | [INFO] [stderr] 521 | pub index: Box, [INFO] [stderr] | ^^^^^^^^^^^^^^ help: use `dyn`: `dyn BwaIndexStruct` [INFO] [stderr] | [INFO] [stderr] = note: #[warn(bare_trait_objects)] on by default [INFO] [stderr] [INFO] [stderr] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stderr] --> src/coverage_takers.rs:6:31 [INFO] [stderr] | [INFO] [stderr] 6 | print_stream: &'a mut std::io::Write, [INFO] [stderr] | ^^^^^^^^^^^^^^ help: use `dyn`: `dyn std::io::Write` [INFO] [stderr] [INFO] [stderr] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stderr] --> src/coverage_takers.rs:10:31 [INFO] [stderr] | [INFO] [stderr] 10 | print_stream: &'a mut std::io::Write, [INFO] [stderr] | ^^^^^^^^^^^^^^ help: use `dyn`: `dyn std::io::Write` [INFO] [stderr] [INFO] [stderr] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stderr] --> src/coverage_takers.rs:46:28 [INFO] [stderr] | [INFO] [stderr] 46 | print_stream: &mut std::io::Write) -> CoverageTakerType { [INFO] [stderr] | ^^^^^^^^^^^^^^ help: use `dyn`: `dyn std::io::Write` [INFO] [stderr] [INFO] [stderr] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stderr] --> src/coverage_takers.rs:53:28 [INFO] [stderr] | [INFO] [stderr] 53 | print_stream: &mut std::io::Write) -> CoverageTakerType { [INFO] [stderr] | ^^^^^^^^^^^^^^ help: use `dyn`: `dyn std::io::Write` [INFO] [stderr] [INFO] [stderr] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stderr] --> src/coverage_printer.rs:20:28 [INFO] [stderr] | [INFO] [stderr] 20 | print_stream: &mut std::io::Write, [INFO] [stderr] | ^^^^^^^^^^^^^^ help: use `dyn`: `dyn std::io::Write` [INFO] [stderr] [INFO] [stderr] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stderr] --> src/coverage_printer.rs:97:28 [INFO] [stderr] | [INFO] [stderr] 97 | print_stream: &mut std::io::Write) { [INFO] [stderr] | ^^^^^^^^^^^^^^ help: use `dyn`: `dyn std::io::Write` [INFO] [stderr] [INFO] [stderr] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stderr] --> src/coverage_printer.rs:126:24 [INFO] [stderr] | [INFO] [stderr] 126 | print_stream: &mut std::io::Write, [INFO] [stderr] | ^^^^^^^^^^^^^^ help: use `dyn`: `dyn std::io::Write` [INFO] [stderr] [INFO] [stderr] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stderr] --> src/coverage_printer.rs:253:24 [INFO] [stderr] | [INFO] [stderr] 253 | print_stream: &mut std::io::Write, [INFO] [stderr] | ^^^^^^^^^^^^^^ help: use `dyn`: `dyn std::io::Write` [INFO] [stderr] [INFO] [stderr] warning: variable does not need to be mutable [INFO] [stderr] --> src/contig.rs:71:36 [INFO] [stderr] | [INFO] [stderr] 71 | for (coverage, mut estimator) in coverages.iter().zip(coverage_estimators.iter_mut()) { [INFO] [stderr] | ----^^^^^^^^^ [INFO] [stderr] | | [INFO] [stderr] | help: remove this `mut` [INFO] [stderr] | [INFO] [stderr] = note: #[warn(unused_mut)] on by default [INFO] [stderr] [INFO] [stderr] warning: variable does not need to be mutable [INFO] [stderr] --> src/contig.rs:23:9 [INFO] [stderr] | [INFO] [stderr] 23 | for mut bam_generator in bam_readers { [INFO] [stderr] | ----^^^^^^^^^^^^^ [INFO] [stderr] | | [INFO] [stderr] | help: remove this `mut` [INFO] [stderr] [INFO] [stderr] warning: variable does not need to be mutable [INFO] [stderr] --> src/genome.rs:27:9 [INFO] [stderr] | [INFO] [stderr] 27 | for mut bam_generator in bam_readers { [INFO] [stderr] | ----^^^^^^^^^^^^^ [INFO] [stderr] | | [INFO] [stderr] | help: remove this `mut` [INFO] [stderr] [INFO] [stderr] warning: variable does not need to be mutable [INFO] [stderr] --> src/genome.rs:350:9 [INFO] [stderr] | [INFO] [stderr] 350 | for mut bam_generator in bam_readers { [INFO] [stderr] | ----^^^^^^^^^^^^^ [INFO] [stderr] | | [INFO] [stderr] | help: remove this `mut` [INFO] [stderr] [INFO] [stderr] warning: variable does not need to be mutable [INFO] [stderr] --> src/coverage_takers.rs:325:33 [INFO] [stderr] | [INFO] [stderr] 325 | let mut struct_to_return; [INFO] [stderr] | ----^^^^^^^^^^^^^^^^ [INFO] [stderr] | | [INFO] [stderr] | help: remove this `mut` [INFO] [stderr] [INFO] [stderr] warning: variable does not need to be mutable [INFO] [stderr] --> src/coverage_printer.rs:282:17 [INFO] [stderr] | [INFO] [stderr] 282 | let mut coverage_multipliers: Vec = [INFO] [stderr] | ----^^^^^^^^^^^^^^^^^^^^ [INFO] [stderr] | | [INFO] [stderr] | help: remove this `mut` [INFO] [stderr] [INFO] [stderr] warning: variable does not need to be mutable [INFO] [stderr] --> src/contig.rs:71:36 [INFO] [stderr] | [INFO] [stderr] 71 | for (coverage, mut estimator) in coverages.iter().zip(coverage_estimators.iter_mut()) { [INFO] [stderr] | ----^^^^^^^^^ [INFO] [stderr] | | [INFO] [stderr] | help: remove this `mut` [INFO] [stderr] | [INFO] [stderr] = note: #[warn(unused_mut)] on by default [INFO] [stderr] [INFO] [stderr] warning: variable does not need to be mutable [INFO] [stderr] --> src/contig.rs:23:9 [INFO] [stderr] | [INFO] [stderr] 23 | for mut bam_generator in bam_readers { [INFO] [stderr] | ----^^^^^^^^^^^^^ [INFO] [stderr] | | [INFO] [stderr] | help: remove this `mut` [INFO] [stderr] [INFO] [stderr] warning: variable does not need to be mutable [INFO] [stderr] --> src/genome.rs:27:9 [INFO] [stderr] | [INFO] [stderr] 27 | for mut bam_generator in bam_readers { [INFO] [stderr] | ----^^^^^^^^^^^^^ [INFO] [stderr] | | [INFO] [stderr] | help: remove this `mut` [INFO] [stderr] [INFO] [stderr] warning: variable does not need to be mutable [INFO] [stderr] --> src/genome.rs:350:9 [INFO] [stderr] | [INFO] [stderr] 350 | for mut bam_generator in bam_readers { [INFO] [stderr] | ----^^^^^^^^^^^^^ [INFO] [stderr] | | [INFO] [stderr] | help: remove this `mut` [INFO] [stderr] [INFO] [stderr] warning: variable does not need to be mutable [INFO] [stderr] --> src/coverage_takers.rs:325:33 [INFO] [stderr] | [INFO] [stderr] 325 | let mut struct_to_return; [INFO] [stderr] | ----^^^^^^^^^^^^^^^^ [INFO] [stderr] | | [INFO] [stderr] | help: remove this `mut` [INFO] [stderr] [INFO] [stderr] warning: variable does not need to be mutable [INFO] [stderr] --> src/coverage_printer.rs:282:17 [INFO] [stderr] | [INFO] [stderr] 282 | let mut coverage_multipliers: Vec = [INFO] [stderr] | ----^^^^^^^^^^^^^^^^^^^^ [INFO] [stderr] | | [INFO] [stderr] | help: remove this `mut` [INFO] [stderr] [INFO] [stderr] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stderr] --> src/main.rs:675:28 [INFO] [stderr] | [INFO] [stderr] 675 | print_stream: &mut std::io::Write) -> Self { [INFO] [stderr] | ^^^^^^^^^^^^^^ help: use `dyn`: `dyn std::io::Write` [INFO] [stderr] | [INFO] [stderr] = note: #[warn(bare_trait_objects)] on by default [INFO] [stderr] [INFO] [stderr] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stderr] --> src/main.rs:675:28 [INFO] [stderr] | [INFO] [stderr] 675 | print_stream: &mut std::io::Write) -> Self { [INFO] [stderr] | ^^^^^^^^^^^^^^ help: use `dyn`: `dyn std::io::Write` [INFO] [stderr] | [INFO] [stderr] = note: #[warn(bare_trait_objects)] on by default [INFO] [stderr] [INFO] [stderr] warning: variable does not need to be mutable [INFO] [stderr] --> src/main.rs:362:25 [INFO] [stderr] | [INFO] [stderr] 362 | let mut bam_readers = coverm::bam_generator::generate_filtered_bam_readers_from_bam_files( [INFO] [stderr] | ----^^^^^^^^^^^ [INFO] [stderr] | | [INFO] [stderr] | help: remove this `mut` [INFO] [stderr] | [INFO] [stderr] = note: #[warn(unused_mut)] on by default [INFO] [stderr] [INFO] [stderr] warning: variable does not need to be mutable [INFO] [stderr] --> src/main.rs:377:25 [INFO] [stderr] | [INFO] [stderr] 377 | let mut bam_readers = coverm::bam_generator::generate_named_bam_readers_from_bam_files( [INFO] [stderr] | ----^^^^^^^^^^^ [INFO] [stderr] | | [INFO] [stderr] | help: remove this `mut` [INFO] [stderr] [INFO] [stderr] warning: variable does not need to be mutable [INFO] [stderr] --> src/main.rs:443:21 [INFO] [stderr] | [INFO] [stderr] 443 | let mut reader = bam::Reader::from_path(bam).expect( [INFO] [stderr] | ----^^^^^^ [INFO] [stderr] | | [INFO] [stderr] | help: remove this `mut` [INFO] [stderr] [INFO] [stderr] warning: variable does not need to be mutable [INFO] [stderr] --> src/main.rs:786:17 [INFO] [stderr] | [INFO] [stderr] 786 | let mut genome_fasta_files: Vec = parse_list_of_genome_fasta_files(m); [INFO] [stderr] | ----^^^^^^^^^^^^^^^^^^ [INFO] [stderr] | | [INFO] [stderr] | help: remove this `mut` [INFO] [stderr] [INFO] [stderr] warning: variable does not need to be mutable [INFO] [stderr] --> src/main.rs:362:25 [INFO] [stderr] | [INFO] [stderr] 362 | let mut bam_readers = coverm::bam_generator::generate_filtered_bam_readers_from_bam_files( [INFO] [stderr] | ----^^^^^^^^^^^ [INFO] [stderr] | | [INFO] [stderr] | help: remove this `mut` [INFO] [stderr] | [INFO] [stderr] = note: #[warn(unused_mut)] on by default [INFO] [stderr] [INFO] [stderr] warning: variable does not need to be mutable [INFO] [stderr] --> src/main.rs:377:25 [INFO] [stderr] | [INFO] [stderr] 377 | let mut bam_readers = coverm::bam_generator::generate_named_bam_readers_from_bam_files( [INFO] [stderr] | ----^^^^^^^^^^^ [INFO] [stderr] | | [INFO] [stderr] | help: remove this `mut` [INFO] [stderr] [INFO] [stderr] warning: variable does not need to be mutable [INFO] [stderr] --> src/main.rs:443:21 [INFO] [stderr] | [INFO] [stderr] 443 | let mut reader = bam::Reader::from_path(bam).expect( [INFO] [stderr] | ----^^^^^^ [INFO] [stderr] | | [INFO] [stderr] | help: remove this `mut` [INFO] [stderr] [INFO] [stderr] warning: variable does not need to be mutable [INFO] [stderr] --> src/main.rs:786:17 [INFO] [stderr] | [INFO] [stderr] 786 | let mut genome_fasta_files: Vec = parse_list_of_genome_fasta_files(m); [INFO] [stderr] | ----^^^^^^^^^^^^^^^^^^ [INFO] [stderr] | | [INFO] [stderr] | help: remove this `mut` [INFO] [stderr] [INFO] [stderr] Finished dev [unoptimized + debuginfo] target(s) in 1m 57s [INFO] running `"docker" "inspect" "d57721067321c230bae8e35041305f76fc139e2a0aa06af55ef973c5be6e5a61"` [INFO] running `"docker" "rm" "-f" "d57721067321c230bae8e35041305f76fc139e2a0aa06af55ef973c5be6e5a61"` [INFO] [stdout] d57721067321c230bae8e35041305f76fc139e2a0aa06af55ef973c5be6e5a61