[INFO] fetching crate varlociraptor 8.8.2... [INFO] checking varlociraptor-8.8.2 against try#4f260f0f20b3133d20cfb50353c0221943af5796+rustflags=-Dunmustuse_in_always_ok for pr-148577 [INFO] extracting crate varlociraptor 8.8.2 into /workspace/builds/worker-2-tc2/source [INFO] started tweaking crates.io crate varlociraptor 8.8.2 [INFO] finished tweaking crates.io crate varlociraptor 8.8.2 [INFO] tweaked toml for crates.io crate varlociraptor 8.8.2 written to /workspace/builds/worker-2-tc2/source/Cargo.toml [INFO] validating manifest of crates.io crate varlociraptor 8.8.2 on toolchain 4f260f0f20b3133d20cfb50353c0221943af5796 [INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+4f260f0f20b3133d20cfb50353c0221943af5796" "metadata" "--manifest-path" "Cargo.toml" "--no-deps", kill_on_drop: false }` [INFO] crate crates.io crate varlociraptor 8.8.2 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" "+4f260f0f20b3133d20cfb50353c0221943af5796" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }` [INFO] [stderr] Blocking waiting for file lock on package cache [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-2-tc2/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-2-tc2/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" "+4f260f0f20b3133d20cfb50353c0221943af5796" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }` [INFO] [stdout] b34c31179575a08db8b7d68de3e17605d01b8fd6a61adebee131bdde390548f3 [INFO] running `Command { std: "docker" "start" "-a" "b34c31179575a08db8b7d68de3e17605d01b8fd6a61adebee131bdde390548f3", kill_on_drop: false }` [INFO] running `Command { std: "docker" "inspect" "b34c31179575a08db8b7d68de3e17605d01b8fd6a61adebee131bdde390548f3", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "b34c31179575a08db8b7d68de3e17605d01b8fd6a61adebee131bdde390548f3", kill_on_drop: false }` [INFO] [stdout] b34c31179575a08db8b7d68de3e17605d01b8fd6a61adebee131bdde390548f3 [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-2-tc2/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-2-tc2/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 -Dunmustuse_in_always_ok" "-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" "+4f260f0f20b3133d20cfb50353c0221943af5796" "check" "--frozen" "--all" "--all-targets" "--message-format=json", kill_on_drop: false }` [INFO] [stdout] e3f7c27fdbee7797475ec71c0c21051cb1e22df33da6d022d1ce44c86d1f2be3 [INFO] running `Command { std: "docker" "start" "-a" "e3f7c27fdbee7797475ec71c0c21051cb1e22df33da6d022d1ce44c86d1f2be3", kill_on_drop: false }` [INFO] [stderr] Compiling serde_core v1.0.228 [INFO] [stderr] Compiling syn v2.0.110 [INFO] [stderr] Compiling syn v1.0.109 [INFO] [stderr] Checking num-integer v0.1.46 [INFO] [stderr] Compiling glob v0.3.3 [INFO] [stderr] Compiling nom v7.1.3 [INFO] [stderr] Compiling openssl-src v300.5.4+3.5.4 [INFO] [stderr] Compiling cmake v0.1.54 [INFO] [stderr] Compiling libz-sys v1.1.22 [INFO] [stderr] Compiling aho-corasick v1.1.4 [INFO] [stderr] Compiling openssl-sys v0.9.111 [INFO] [stderr] Compiling libloading v0.8.9 [INFO] [stderr] Compiling clang-sys v1.8.1 [INFO] [stderr] Compiling ahash v0.7.8 [INFO] [stderr] Compiling matrixmultiply v0.3.10 [INFO] [stderr] Compiling regex-automata v0.4.13 [INFO] [stderr] Compiling bindgen v0.69.5 [INFO] [stderr] Compiling semver v0.1.20 [INFO] [stderr] Checking bytemuck v1.24.0 [INFO] [stderr] Compiling rustc_version v0.1.7 [INFO] [stderr] Compiling cexpr v0.6.0 [INFO] [stderr] Checking safe_arch v0.7.4 [INFO] [stderr] Compiling darling_core v0.14.4 [INFO] [stderr] Compiling itertools v0.12.1 [INFO] [stderr] Checking num-complex v0.4.6 [INFO] [stderr] Compiling regex v1.12.2 [INFO] [stderr] Compiling curl-sys v0.4.84+curl-8.17.0 [INFO] [stderr] Compiling synstructure v0.13.2 [INFO] [stderr] Compiling quick-error v1.2.3 [INFO] [stderr] Compiling fs-utils v1.1.4 [INFO] [stderr] Compiling darling_macro v0.14.4 [INFO] [stderr] Compiling darling v0.14.4 [INFO] [stderr] Checking wide v0.7.33 [INFO] [stderr] Compiling newtype_derive v0.1.6 [INFO] [stderr] Checking approx v0.5.1 [INFO] [stderr] Compiling feature-probe v0.1.1 [INFO] [stderr] Checking futures-core v0.3.31 [INFO] [stderr] Checking futures-sink v0.3.31 [INFO] [stderr] Compiling bv v0.11.1 [INFO] [stderr] Compiling num-traits v0.2.19 [INFO] [stderr] Checking hashbrown v0.12.3 [INFO] [stderr] Compiling proc-macro-error-attr v1.0.4 [INFO] [stderr] Checking num-iter v0.1.45 [INFO] [stderr] Checking num-rational v0.4.2 [INFO] [stderr] Compiling sysinfo v0.15.9 [INFO] [stderr] Compiling jemalloc-sys v0.5.4+5.3.0-patched [INFO] [stderr] Compiling serde_derive v1.0.228 [INFO] [stderr] Compiling zerofrom-derive v0.1.6 [INFO] [stderr] Compiling yoke-derive v0.8.1 [INFO] [stderr] Compiling zerovec-derive v0.11.2 [INFO] [stderr] Compiling displaydoc v0.2.5 [INFO] [stderr] Compiling zerocopy-derive v0.8.27 [INFO] [stderr] Compiling thiserror-impl v1.0.69 [INFO] [stderr] Checking simba v0.9.1 [INFO] [stderr] Compiling derive-new v0.6.0 [INFO] [stderr] Checking zerofrom v0.1.6 [INFO] [stderr] Compiling thiserror-impl v2.0.17 [INFO] [stderr] Checking yoke v0.8.1 [INFO] [stderr] Checking zerovec v0.11.5 [INFO] [stderr] Checking zerocopy v0.8.27 [INFO] [stderr] Checking tinystr v0.8.2 [INFO] [stderr] Checking potential_utf v0.1.4 [INFO] [stderr] Checking zerotrie v0.2.3 [INFO] [stderr] Checking icu_locale_core v2.1.1 [INFO] [stderr] Checking icu_collections v2.1.1 [INFO] [stderr] Checking thiserror v1.0.69 [INFO] [stderr] Compiling strum_macros v0.26.4 [INFO] [stderr] Compiling GSL-sys v3.0.0 [INFO] [stderr] Checking futures-task v0.3.31 [INFO] [stderr] Compiling askama_escape v0.10.3 [INFO] [stderr] Checking icu_provider v2.1.1 [INFO] [stderr] Compiling anyhow v1.0.100 [INFO] [stderr] Checking ppv-lite86 v0.2.21 [INFO] [stderr] Compiling humansize v1.1.1 [INFO] [stderr] Checking icu_normalizer v2.1.1 [INFO] [stderr] Checking icu_properties v2.1.1 [INFO] [stderr] Checking rand_chacha v0.3.1 [INFO] [stderr] Checking rand v0.8.5 [INFO] [stderr] Checking serde v1.0.228 [INFO] [stderr] Checking rand_distr v0.4.3 [INFO] [stderr] Checking futures-util v0.3.31 [INFO] [stderr] Checking vec_map v0.8.2 [INFO] [stderr] Compiling toml v0.5.11 [INFO] [stderr] Checking idna_adapter v1.2.1 [INFO] [stderr] Checking bio-types v1.0.4 [INFO] [stderr] Checking idna v1.1.0 [INFO] [stderr] Checking hashbrown v0.15.5 [INFO] [stderr] Checking nalgebra v0.33.2 [INFO] [stderr] Compiling hts-sys v2.2.0 [INFO] [stderr] Compiling askama_shared v0.12.2 [INFO] [stderr] Checking thiserror v2.0.17 [INFO] [stderr] Compiling tokio-macros v2.6.0 [INFO] [stderr] Compiling enum-map-derive v0.17.0 [INFO] [stderr] Checking num v0.1.43 [INFO] [stderr] Compiling proc-macro-error v1.0.4 [INFO] [stderr] Checking futures-channel v0.3.31 [INFO] [stderr] Checking lzma-sys v0.1.20 [INFO] [stderr] Compiling derive_builder_core v0.12.0 [INFO] [stderr] Compiling ring v0.16.20 [INFO] [stderr] Compiling proc-macro-error-attr2 v2.0.0 [INFO] [stderr] Checking bit-vec v0.8.0 [INFO] [stderr] Compiling cached_proc_macro_types v0.1.1 [INFO] [stderr] Checking yaml-rust v0.3.5 [INFO] [stderr] Checking custom_derive v0.1.7 [INFO] [stderr] Checking futures-io v0.3.31 [INFO] [stderr] Checking futures v0.3.31 [INFO] [stderr] Checking clap v2.34.0 [INFO] [stderr] Checking bit-set v0.8.0 [INFO] [stderr] Checking yaml-rust v0.4.5 [INFO] [stderr] Checking petgraph v0.8.3 [INFO] [stderr] Compiling derive_builder_macro v0.12.0 [INFO] [stderr] Checking deranged v0.5.5 [INFO] [stderr] Compiling cached_proc_macro v0.16.0 [INFO] [stderr] Compiling askama_derive v0.11.2 [INFO] [stderr] Compiling proc-macro-error2 v2.0.1 [INFO] [stderr] Checking rand v0.3.23 [INFO] [stderr] Checking csv v1.4.0 [INFO] [stderr] Compiling structopt-derive v0.4.18 [INFO] [stderr] Checking url v2.5.7 [INFO] [stderr] Compiling pest_generator v2.8.3 [INFO] [stderr] Checking tokio v1.48.0 [INFO] [stderr] Checking enum-map v2.7.3 [INFO] [stderr] Checking rulinalg v0.3.7 [INFO] [stderr] Checking indexmap v1.9.3 [INFO] [stderr] Checking multimap v0.10.1 [INFO] [stderr] Checking ndarray v0.16.1 [INFO] [stderr] Checking serde_json v1.0.145 [INFO] [stderr] Checking getrandom v0.3.4 [INFO] [stderr] Compiling derive-new v0.7.0 [INFO] [stderr] Compiling typed-builder-macro v0.20.1 [INFO] [stderr] Checking statrs v0.18.0 [INFO] [stderr] Compiling async-trait v0.1.89 [INFO] [stderr] Checking itertools v0.9.0 [INFO] [stderr] Compiling itertools v0.8.2 [INFO] [stderr] Checking itertools-num v0.1.3 [INFO] [stderr] Checking instant v0.1.13 [INFO] [stderr] Checking editdistancek v1.0.2 [INFO] [stderr] Checking triple_accel v0.4.0 [INFO] [stderr] Checking bytecount v0.6.9 [INFO] [stderr] Checking linear-map v1.2.0 [INFO] [stderr] Checking async_once v0.2.6 [INFO] [stderr] Checking ieee754 v0.2.6 [INFO] [stderr] Checking eval v0.4.3 [INFO] [stderr] Compiling shrinkwraprs v0.3.0 [INFO] [stderr] Checking typed-builder v0.20.1 [INFO] [stderr] Checking cached v0.42.0 [INFO] [stderr] Checking tempfile v3.23.0 [INFO] [stderr] Checking time v0.3.44 [INFO] [stderr] Checking boolean_expression v0.4.4 [INFO] [stderr] Checking rusty-machine v0.5.4 [INFO] [stderr] Checking GSL v6.0.0 [INFO] [stderr] Checking serde_yaml v0.8.26 [INFO] [stderr] Compiling pest_derive v2.8.3 [INFO] [stderr] Checking structopt v0.3.26 [INFO] [stderr] Checking progress-logger v0.3.1 [INFO] [stderr] Checking askama v0.11.1 [INFO] [stderr] Compiling derefable v0.1.0 [INFO] [stderr] Compiling getset v0.1.6 [INFO] [stderr] Checking derive_builder v0.12.0 [INFO] [stderr] Checking bio v2.3.0 [INFO] [stderr] Checking bincode v1.3.3 [INFO] [stderr] Checking half v2.7.1 [INFO] [stderr] Checking ordered-float v1.1.1 [INFO] [stderr] Checking fern v0.6.2 [INFO] [stderr] Checking lru v0.7.8 [INFO] [stderr] Checking uuid v0.8.2 [INFO] [stderr] Checking counter v0.6.0 [INFO] [stderr] Checking auto_ops v0.3.0 [INFO] [stderr] Checking data-encoding v2.9.0 [INFO] [stderr] Checking lru_time_cache v0.11.11 [INFO] [stderr] Checking env_logger v0.9.3 [INFO] [stderr] Checking jemallocator v0.5.4 [INFO] [stderr] Checking rust-htslib v0.49.0 [INFO] [stderr] Checking varlociraptor v8.8.2 (/opt/rustwide/workdir) [INFO] [stdout] error: this type will no longer be must used: std::result::Result [INFO] [stdout] --> src/cli.rs:199:9 [INFO] [stdout] | [INFO] [stdout] 199 | / #[structopt( [INFO] [stdout] 200 | | long, [INFO] [stdout] 201 | | required = true, [INFO] [stdout] 202 | | help = "BAM file with aligned reads from a single sample. BAM file must be indexed (e.g. with samtools index)." [INFO] [stdout] 203 | | )] [INFO] [stdout] 204 | | bam: PathBuf, [INFO] [stdout] | |____________________^ [INFO] [stdout] | [INFO] [stdout] = note: requested on the command line with `-D unmustuse-in-always-ok` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error: this type will no longer be must used: std::result::Result [INFO] [stdout] --> src/cli.rs:205:9 [INFO] [stdout] | [INFO] [stdout] 205 | / ... #[structopt( [INFO] [stdout] 206 | | ... long, [INFO] [stdout] 207 | | ... help = "Name of INFO field containing an expected heterozygosity per variant allele (can be e.g. a population allele frequency)... [INFO] [stdout] 208 | | ... )] [INFO] [stdout] 209 | | ... variant_heterozygosity_field: Option, [INFO] [stdout] | |__________________________________________________^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error: this type will no longer be must used: std::result::Result [INFO] [stdout] --> src/cli.rs:210:9 [INFO] [stdout] | [INFO] [stdout] 210 | / ... #[structopt( [INFO] [stdout] 211 | | ... long, [INFO] [stdout] 212 | | ... help = "Name of INFO field containing an expected somatic effective mutation rate per variant allele (can be e.g. a poplulation... [INFO] [stdout] 213 | | ... )] [INFO] [stdout] 214 | | ... variant_somatic_effective_mutation_rate_field: Option, [INFO] [stdout] | |___________________________________________________________________^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error: this type will no longer be must used: std::result::Result [INFO] [stdout] --> src/cli.rs:262:9 [INFO] [stdout] | [INFO] [stdout] 262 | / #[structopt( [INFO] [stdout] 263 | | long = "alignment-properties", [INFO] [stdout] 264 | | help = "Alignment properties JSON file for sample. If not provided, properties \ [INFO] [stdout] 265 | | will be estimated from the given BAM file. It is recommended to estimate alignment \ [INFO] [stdout] 266 | | properties separately, see 'varlociraptor estimate alignment-properties --help'." [INFO] [stdout] 267 | | )] [INFO] [stdout] 268 | | alignment_properties: Option, [INFO] [stdout] | |_____________________________________________^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error: this type will no longer be must used: std::result::Result [INFO] [stdout] --> src/cli.rs:275:9 [INFO] [stdout] | [INFO] [stdout] 275 | / #[structopt( [INFO] [stdout] 276 | | long = "propagate-info-fields", [INFO] [stdout] 277 | | help = "Additional INFO fields in the input BCF that shall be propagated to the output BCF \ [INFO] [stdout] 278 | | (not supported for variants connected via EVENT tags except breakends)." [INFO] [stdout] 279 | | )] [INFO] [stdout] 280 | | #[serde(default)] [INFO] [stdout] 281 | | propagate_info_fields: Vec, [INFO] [stdout] | |__________________________________________^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error: this type will no longer be must used: std::result::Result [INFO] [stdout] --> src/cli.rs:304:9 [INFO] [stdout] | [INFO] [stdout] 304 | / #[structopt( [INFO] [stdout] 305 | | long = "pairhmm-mode", [INFO] [stdout] 306 | | possible_values = &["fast", "exact", "homopolymer"], [INFO] [stdout] 307 | | default_value = "exact", [INFO] [stdout] ... | [INFO] [stdout] 319 | | #[serde(default = "default_pairhmm_mode")] [INFO] [stdout] 320 | | pairhmm_mode: String, [INFO] [stdout] | |____________________________^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error: this type will no longer be must used: std::result::Result [INFO] [stdout] --> src/cli.rs:321:9 [INFO] [stdout] | [INFO] [stdout] 321 | / #[structopt( [INFO] [stdout] 322 | | long = "log-mode", [INFO] [stdout] 323 | | possible_values = &["default", "each-record"], [INFO] [stdout] 324 | | default_value = "default", [INFO] [stdout] ... | [INFO] [stdout] 329 | | #[serde(default = "default_log_mode")] [INFO] [stdout] 330 | | log_mode: String, [INFO] [stdout] | |________________________^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error: this type will no longer be must used: std::result::Result [INFO] [stdout] --> src/cli.rs:358:9 [INFO] [stdout] | [INFO] [stdout] 358 | / #[structopt( [INFO] [stdout] 359 | | long = "contig", [INFO] [stdout] 360 | | required = true, [INFO] [stdout] 361 | | help = "Contig to consider for ploidy information." [INFO] [stdout] 362 | | )] [INFO] [stdout] 363 | | contig: String, [INFO] [stdout] | |______________________^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error: this type will no longer be must used: std::result::Result [INFO] [stdout] --> src/cli.rs:364:9 [INFO] [stdout] | [INFO] [stdout] 364 | / #[structopt(long = "sample", required = true, help = "Sample to plot.")] [INFO] [stdout] 365 | | sample: String, [INFO] [stdout] | |______________________^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error: this type will no longer be must used: std::result::Result [INFO] [stdout] --> src/cli.rs:375:9 [INFO] [stdout] | [INFO] [stdout] 375 | / #[structopt( [INFO] [stdout] 376 | | long = "sample-x", [INFO] [stdout] 377 | | help = "Name of the first sample in the given VCF/BCF." [INFO] [stdout] 378 | | )] [INFO] [stdout] 379 | | sample_x: String, [INFO] [stdout] | |________________________^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error: this type will no longer be must used: std::result::Result [INFO] [stdout] --> src/cli.rs:380:9 [INFO] [stdout] | [INFO] [stdout] 380 | / #[structopt( [INFO] [stdout] 381 | | long = "sample-y", [INFO] [stdout] 382 | | help = "Name(s) of the alternative sample(s) in the given VCF/BCF. Multiple samples can be given." [INFO] [stdout] 383 | | )] [INFO] [stdout] 384 | | sample_y: Vec, [INFO] [stdout] | |_____________________________^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error: this type will no longer be must used: std::result::Result [INFO] [stdout] --> src/cli.rs:403:9 [INFO] [stdout] | [INFO] [stdout] 403 | / #[structopt( [INFO] [stdout] 404 | | long, [INFO] [stdout] 405 | | required = true, [INFO] [stdout] 406 | | help = "BAM files with aligned reads from a single sample or a set of \ [INFO] [stdout] ... | [INFO] [stdout] 410 | | )] [INFO] [stdout] 411 | | bams: Vec, [INFO] [stdout] | |__________________________^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error: this type will no longer be must used: std::result::Result [INFO] [stdout] --> src/cli.rs:428:9 [INFO] [stdout] | [INFO] [stdout] 428 | / #[structopt(long = "sample", help = "Presumably contaminated sample.")] [INFO] [stdout] 429 | | sample: PathBuf, [INFO] [stdout] | |_______________________^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error: this type will no longer be must used: std::result::Result [INFO] [stdout] --> src/cli.rs:430:9 [INFO] [stdout] | [INFO] [stdout] 430 | / #[structopt(long = "contaminant", help = "Presumably contaminating sample.")] [INFO] [stdout] 431 | | contaminant: PathBuf, [INFO] [stdout] | |____________________________^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error: this type will no longer be must used: std::result::Result [INFO] [stdout] --> src/cli.rs:444:9 [INFO] [stdout] | [INFO] [stdout] 444 | / #[structopt( [INFO] [stdout] 445 | | long = "output", [INFO] [stdout] 446 | | help = "Output file; if not specified, output is printed to STDOUT." [INFO] [stdout] 447 | | )] [INFO] [stdout] 448 | | output: Option, [INFO] [stdout] | |_______________________________^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error: this type will no longer be must used: std::result::Result [INFO] [stdout] --> src/cli.rs:449:9 [INFO] [stdout] | [INFO] [stdout] 449 | / #[structopt( [INFO] [stdout] 450 | | long = "output-plot", [INFO] [stdout] 451 | | help = "Path to store vega-lite plot of contamination/purity." [INFO] [stdout] 452 | | )] [INFO] [stdout] 453 | | output_plot: Option, [INFO] [stdout] | |____________________________________^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error: this type will no longer be must used: std::result::Result [INFO] [stdout] --> src/cli.rs:454:9 [INFO] [stdout] | [INFO] [stdout] 454 | / #[structopt( [INFO] [stdout] 455 | | long = "output-max-vaf-variants", [INFO] [stdout] 456 | | help = "Path to store TSV of variant positions with maximum VAF in the contaminated sample (for QC)." [INFO] [stdout] 457 | | )] [INFO] [stdout] 458 | | output_max_vaf_variants: Option, [INFO] [stdout] | |________________________________________________^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error: this type will no longer be must used: std::result::Result [INFO] [stdout] --> src/cli.rs:472:9 [INFO] [stdout] | [INFO] [stdout] 472 | / #[structopt(long = "events", help = "Events to consider (e.g. SOMATIC_TUMOR).")] [INFO] [stdout] 473 | | events: Vec, [INFO] [stdout] | |___________________________^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error: this type will no longer be must used: std::result::Result [INFO] [stdout] --> src/cli.rs:474:9 [INFO] [stdout] | [INFO] [stdout] 474 | / #[structopt( [INFO] [stdout] 475 | | long = "sample", [INFO] [stdout] 476 | | help = "Name(s) of the sample(s) in the given VCF/BCF. Multiple samples can be given when using the multibar plot mode." [INFO] [stdout] 477 | | )] [INFO] [stdout] 478 | | sample: Vec, [INFO] [stdout] | |___________________________^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error: this type will no longer be must used: std::result::Result [INFO] [stdout] --> src/cli.rs:510:9 [INFO] [stdout] | [INFO] [stdout] 510 | / #[structopt( [INFO] [stdout] 511 | | long = "propagate-info-fields", [INFO] [stdout] 512 | | help = "Additional INFO fields in the input BCF that shall be propagated to the output BCF." [INFO] [stdout] 513 | | )] [INFO] [stdout] 514 | | propagate_info_fields: Vec, [INFO] [stdout] | |__________________________________________^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error: this type will no longer be must used: std::result::Result [INFO] [stdout] --> src/cli.rs:574:9 [INFO] [stdout] | [INFO] [stdout] 574 | / #[structopt( [INFO] [stdout] 575 | | long = "testcase-locus", [INFO] [stdout] 576 | | help = "Create a test case for the given locus. Locus must be given in the form \ [INFO] [stdout] 577 | | CHROM:POS. Alternatively, for single variant VCFs, you can \ [INFO] [stdout] 578 | | specify 'all'." [INFO] [stdout] 579 | | )] [INFO] [stdout] 580 | | testcase_locus: Option, [INFO] [stdout] | |______________________________________^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error: this type will no longer be must used: std::result::Result [INFO] [stdout] --> src/cli.rs:581:9 [INFO] [stdout] | [INFO] [stdout] 581 | / #[structopt( [INFO] [stdout] 582 | | long = "testcase-prefix", [INFO] [stdout] 583 | | help = "Create test case files in the given directory." [INFO] [stdout] 584 | | )] [INFO] [stdout] 585 | | testcase_prefix: Option, [INFO] [stdout] | |_______________________________________^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error: this type will no longer be must used: std::result::Result [INFO] [stdout] --> src/cli.rs:591:9 [INFO] [stdout] | [INFO] [stdout] 591 | / #[structopt( [INFO] [stdout] 592 | | long, [INFO] [stdout] 593 | | short, [INFO] [stdout] 594 | | help = "Output variant calls to given path (in BCF format). If omitted, prints calls to STDOUT." [INFO] [stdout] 595 | | )] [INFO] [stdout] 596 | | output: Option, [INFO] [stdout] | |_______________________________^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error: this type will no longer be must used: std::result::Result [INFO] [stdout] --> src/cli.rs:597:9 [INFO] [stdout] | [INFO] [stdout] 597 | / #[structopt( [INFO] [stdout] 598 | | long = "log-mode", [INFO] [stdout] 599 | | possible_values = &["default", "each-record"], [INFO] [stdout] 600 | | default_value = "default", [INFO] [stdout] ... | [INFO] [stdout] 605 | | #[serde(default = "default_log_mode")] [INFO] [stdout] 606 | | log_mode: String, [INFO] [stdout] | |________________________^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error: this type will no longer be must used: std::result::Result [INFO] [stdout] --> src/cli.rs:692:9 [INFO] [stdout] | [INFO] [stdout] 692 | / ... #[structopt( [INFO] [stdout] 693 | | ... long = "obs", [INFO] [stdout] 694 | | ... required = true, [INFO] [stdout] 695 | | ... help = "BCF file with varlociraptor preprocess results for samples defined in the given scenario (given as samplename=path/to/c... [INFO] [stdout] 696 | | ... )] [INFO] [stdout] 697 | | ... sample_observations: Vec, [INFO] [stdout] | |______________________________________^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error: this type will no longer be must used: std::result::Result [INFO] [stdout] --> src/cli.rs:771:9 [INFO] [stdout] | [INFO] [stdout] 771 | / #[structopt(long, help = "Events to consider.")] [INFO] [stdout] 772 | | events: Vec, [INFO] [stdout] | |___________________________^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error: this type will no longer be must used: std::result::Result [INFO] [stdout] --> src/cli.rs:792:9 [INFO] [stdout] | [INFO] [stdout] 792 | / #[structopt(long, help = "Events to consider.")] [INFO] [stdout] 793 | | events: Vec, [INFO] [stdout] | |___________________________^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error: this type will no longer be must used: std::result::Result [INFO] [stdout] --> src/testcase/runner/common/version0.rs:188:13 [INFO] [stdout] | [INFO] [stdout] 188 | / #[structopt( [INFO] [stdout] 189 | | long = "somatic-tumor-events", [INFO] [stdout] 190 | | default_value = "SOMATIC_TUMOR", [INFO] [stdout] 191 | | help = "Events to consider (e.g. SOMATIC_TUMOR)." [INFO] [stdout] 192 | | )] [INFO] [stdout] 193 | | somatic_tumor_events: Vec, [INFO] [stdout] | |_____________________________________________^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error: this type will no longer be must used: std::result::Result [INFO] [stdout] --> src/testcase/runner/common/version0.rs:194:13 [INFO] [stdout] | [INFO] [stdout] 194 | / #[structopt( [INFO] [stdout] 195 | | long = "tumor-sample", [INFO] [stdout] 196 | | default_value = "tumor", [INFO] [stdout] 197 | | help = "Name of the tumor sample in the given VCF/BCF." [INFO] [stdout] 198 | | )] [INFO] [stdout] 199 | | tumor_sample: String, [INFO] [stdout] | |________________________________^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error: this type will no longer be must used: std::result::Result [INFO] [stdout] --> src/testcase/runner/common/version0.rs:286:13 [INFO] [stdout] | [INFO] [stdout] 286 | / #[structopt( [INFO] [stdout] 287 | | long = "testcase-locus", [INFO] [stdout] 288 | | help = "Create a test case for the given locus. Locus must be given in the form \ [INFO] [stdout] 289 | | CHROM:POS[:IDX]. IDX is thereby an optional value to select a particular \ [INFO] [stdout] ... | [INFO] [stdout] 293 | | )] [INFO] [stdout] 294 | | testcase_locus: Option, [INFO] [stdout] | |__________________________________________^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error: this type will no longer be must used: std::result::Result [INFO] [stdout] --> src/testcase/runner/common/version0.rs:295:13 [INFO] [stdout] | [INFO] [stdout] 295 | / #[structopt( [INFO] [stdout] 296 | | long = "testcase-prefix", [INFO] [stdout] 297 | | help = "Create test case files in the given directory." [INFO] [stdout] 298 | | )] [INFO] [stdout] 299 | | testcase_prefix: Option, [INFO] [stdout] | |___________________________________________^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error: this type will no longer be must used: std::result::Result [INFO] [stdout] --> src/testcase/runner/common/version0.rs:388:13 [INFO] [stdout] | [INFO] [stdout] 388 | / #[structopt(long, help = "BAM files with aligned reads for each sample.")] [INFO] [stdout] 389 | | bams: Vec, [INFO] [stdout] | |_____________________________^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error: this type will no longer be must used: std::result::Result [INFO] [stdout] --> src/testcase/runner/common/version0.rs:390:13 [INFO] [stdout] | [INFO] [stdout] 390 | / #[structopt( [INFO] [stdout] 391 | | long = "alignment-properties", [INFO] [stdout] 392 | | help = "Alignment properties JSON file for normal sample. If not provided, properties \ [INFO] [stdout] 393 | | will be estimated from the given BAM file." [INFO] [stdout] 394 | | )] [INFO] [stdout] 395 | | alignment_properties: Vec, [INFO] [stdout] | |_____________________________________________^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error: this type will no longer be must used: std::result::Result [INFO] [stdout] --> src/testcase/runner/common/version0.rs:419:13 [INFO] [stdout] | [INFO] [stdout] 419 | / #[structopt(long, help = "Events to consider.")] [INFO] [stdout] 420 | | events: Vec, [INFO] [stdout] | |_______________________________^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error: this type will no longer be must used: std::result::Result [INFO] [stdout] --> src/testcase/runner/common/version0.rs:439:13 [INFO] [stdout] | [INFO] [stdout] 439 | / #[structopt(long, help = "Events to consider.")] [INFO] [stdout] 440 | | events: Vec, [INFO] [stdout] | |_______________________________^ [INFO] [stdout] [INFO] [stdout] [INFO] [stderr] error: could not compile `varlociraptor` (lib test) due to 35 previous errors [INFO] [stderr] warning: build failed, waiting for other jobs to finish... [INFO] [stdout] error: this type will no longer be must used: std::result::Result [INFO] [stdout] --> src/cli.rs:199:9 [INFO] [stdout] | [INFO] [stdout] 199 | / #[structopt( [INFO] [stdout] 200 | | long, [INFO] [stdout] 201 | | required = true, [INFO] [stdout] 202 | | help = "BAM file with aligned reads from a single sample. BAM file must be indexed (e.g. with samtools index)." [INFO] [stdout] 203 | | )] [INFO] [stdout] 204 | | bam: PathBuf, [INFO] [stdout] | |____________________^ [INFO] [stdout] | [INFO] [stdout] = note: requested on the command line with `-D unmustuse-in-always-ok` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error: this type will no longer be must used: std::result::Result [INFO] [stdout] --> src/cli.rs:205:9 [INFO] [stdout] | [INFO] [stdout] 205 | / ... #[structopt( [INFO] [stdout] 206 | | ... long, [INFO] [stdout] 207 | | ... help = "Name of INFO field containing an expected heterozygosity per variant allele (can be e.g. a population allele frequency)... [INFO] [stdout] 208 | | ... )] [INFO] [stdout] 209 | | ... variant_heterozygosity_field: Option, [INFO] [stdout] | |__________________________________________________^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error: this type will no longer be must used: std::result::Result [INFO] [stdout] --> src/cli.rs:210:9 [INFO] [stdout] | [INFO] [stdout] 210 | / ... #[structopt( [INFO] [stdout] 211 | | ... long, [INFO] [stdout] 212 | | ... help = "Name of INFO field containing an expected somatic effective mutation rate per variant allele (can be e.g. a poplulation... [INFO] [stdout] 213 | | ... )] [INFO] [stdout] 214 | | ... variant_somatic_effective_mutation_rate_field: Option, [INFO] [stdout] | |___________________________________________________________________^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error: this type will no longer be must used: std::result::Result [INFO] [stdout] --> src/cli.rs:262:9 [INFO] [stdout] | [INFO] [stdout] 262 | / #[structopt( [INFO] [stdout] 263 | | long = "alignment-properties", [INFO] [stdout] 264 | | help = "Alignment properties JSON file for sample. If not provided, properties \ [INFO] [stdout] 265 | | will be estimated from the given BAM file. It is recommended to estimate alignment \ [INFO] [stdout] 266 | | properties separately, see 'varlociraptor estimate alignment-properties --help'." [INFO] [stdout] 267 | | )] [INFO] [stdout] 268 | | alignment_properties: Option, [INFO] [stdout] | |_____________________________________________^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error: this type will no longer be must used: std::result::Result [INFO] [stdout] --> src/cli.rs:275:9 [INFO] [stdout] | [INFO] [stdout] 275 | / #[structopt( [INFO] [stdout] 276 | | long = "propagate-info-fields", [INFO] [stdout] 277 | | help = "Additional INFO fields in the input BCF that shall be propagated to the output BCF \ [INFO] [stdout] 278 | | (not supported for variants connected via EVENT tags except breakends)." [INFO] [stdout] 279 | | )] [INFO] [stdout] 280 | | #[serde(default)] [INFO] [stdout] 281 | | propagate_info_fields: Vec, [INFO] [stdout] | |__________________________________________^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error: this type will no longer be must used: std::result::Result [INFO] [stdout] --> src/cli.rs:304:9 [INFO] [stdout] | [INFO] [stdout] 304 | / #[structopt( [INFO] [stdout] 305 | | long = "pairhmm-mode", [INFO] [stdout] 306 | | possible_values = &["fast", "exact", "homopolymer"], [INFO] [stdout] 307 | | default_value = "exact", [INFO] [stdout] ... | [INFO] [stdout] 319 | | #[serde(default = "default_pairhmm_mode")] [INFO] [stdout] 320 | | pairhmm_mode: String, [INFO] [stdout] | |____________________________^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error: this type will no longer be must used: std::result::Result [INFO] [stdout] --> src/cli.rs:321:9 [INFO] [stdout] | [INFO] [stdout] 321 | / #[structopt( [INFO] [stdout] 322 | | long = "log-mode", [INFO] [stdout] 323 | | possible_values = &["default", "each-record"], [INFO] [stdout] 324 | | default_value = "default", [INFO] [stdout] ... | [INFO] [stdout] 329 | | #[serde(default = "default_log_mode")] [INFO] [stdout] 330 | | log_mode: String, [INFO] [stdout] | |________________________^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error: this type will no longer be must used: std::result::Result [INFO] [stdout] --> src/cli.rs:358:9 [INFO] [stdout] | [INFO] [stdout] 358 | / #[structopt( [INFO] [stdout] 359 | | long = "contig", [INFO] [stdout] 360 | | required = true, [INFO] [stdout] 361 | | help = "Contig to consider for ploidy information." [INFO] [stdout] 362 | | )] [INFO] [stdout] 363 | | contig: String, [INFO] [stdout] | |______________________^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error: this type will no longer be must used: std::result::Result [INFO] [stdout] --> src/cli.rs:364:9 [INFO] [stdout] | [INFO] [stdout] 364 | / #[structopt(long = "sample", required = true, help = "Sample to plot.")] [INFO] [stdout] 365 | | sample: String, [INFO] [stdout] | |______________________^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error: this type will no longer be must used: std::result::Result [INFO] [stdout] --> src/cli.rs:375:9 [INFO] [stdout] | [INFO] [stdout] 375 | / #[structopt( [INFO] [stdout] 376 | | long = "sample-x", [INFO] [stdout] 377 | | help = "Name of the first sample in the given VCF/BCF." [INFO] [stdout] 378 | | )] [INFO] [stdout] 379 | | sample_x: String, [INFO] [stdout] | |________________________^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error: this type will no longer be must used: std::result::Result [INFO] [stdout] --> src/cli.rs:380:9 [INFO] [stdout] | [INFO] [stdout] 380 | / #[structopt( [INFO] [stdout] 381 | | long = "sample-y", [INFO] [stdout] 382 | | help = "Name(s) of the alternative sample(s) in the given VCF/BCF. Multiple samples can be given." [INFO] [stdout] 383 | | )] [INFO] [stdout] 384 | | sample_y: Vec, [INFO] [stdout] | |_____________________________^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error: this type will no longer be must used: std::result::Result [INFO] [stdout] --> src/cli.rs:403:9 [INFO] [stdout] | [INFO] [stdout] 403 | / #[structopt( [INFO] [stdout] 404 | | long, [INFO] [stdout] 405 | | required = true, [INFO] [stdout] 406 | | help = "BAM files with aligned reads from a single sample or a set of \ [INFO] [stdout] ... | [INFO] [stdout] 410 | | )] [INFO] [stdout] 411 | | bams: Vec, [INFO] [stdout] | |__________________________^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error: this type will no longer be must used: std::result::Result [INFO] [stdout] --> src/cli.rs:428:9 [INFO] [stdout] | [INFO] [stdout] 428 | / #[structopt(long = "sample", help = "Presumably contaminated sample.")] [INFO] [stdout] 429 | | sample: PathBuf, [INFO] [stdout] | |_______________________^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error: this type will no longer be must used: std::result::Result [INFO] [stdout] --> src/cli.rs:430:9 [INFO] [stdout] | [INFO] [stdout] 430 | / #[structopt(long = "contaminant", help = "Presumably contaminating sample.")] [INFO] [stdout] 431 | | contaminant: PathBuf, [INFO] [stdout] | |____________________________^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error: this type will no longer be must used: std::result::Result [INFO] [stdout] --> src/cli.rs:444:9 [INFO] [stdout] | [INFO] [stdout] 444 | / #[structopt( [INFO] [stdout] 445 | | long = "output", [INFO] [stdout] 446 | | help = "Output file; if not specified, output is printed to STDOUT." [INFO] [stdout] 447 | | )] [INFO] [stdout] 448 | | output: Option, [INFO] [stdout] | |_______________________________^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error: this type will no longer be must used: std::result::Result [INFO] [stdout] --> src/cli.rs:449:9 [INFO] [stdout] | [INFO] [stdout] 449 | / #[structopt( [INFO] [stdout] 450 | | long = "output-plot", [INFO] [stdout] 451 | | help = "Path to store vega-lite plot of contamination/purity." [INFO] [stdout] 452 | | )] [INFO] [stdout] 453 | | output_plot: Option, [INFO] [stdout] | |____________________________________^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error: this type will no longer be must used: std::result::Result [INFO] [stdout] --> src/cli.rs:454:9 [INFO] [stdout] | [INFO] [stdout] 454 | / #[structopt( [INFO] [stdout] 455 | | long = "output-max-vaf-variants", [INFO] [stdout] 456 | | help = "Path to store TSV of variant positions with maximum VAF in the contaminated sample (for QC)." [INFO] [stdout] 457 | | )] [INFO] [stdout] 458 | | output_max_vaf_variants: Option, [INFO] [stdout] | |________________________________________________^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error: this type will no longer be must used: std::result::Result [INFO] [stdout] --> src/cli.rs:472:9 [INFO] [stdout] | [INFO] [stdout] 472 | / #[structopt(long = "events", help = "Events to consider (e.g. SOMATIC_TUMOR).")] [INFO] [stdout] 473 | | events: Vec, [INFO] [stdout] | |___________________________^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error: this type will no longer be must used: std::result::Result [INFO] [stdout] --> src/cli.rs:474:9 [INFO] [stdout] | [INFO] [stdout] 474 | / #[structopt( [INFO] [stdout] 475 | | long = "sample", [INFO] [stdout] 476 | | help = "Name(s) of the sample(s) in the given VCF/BCF. Multiple samples can be given when using the multibar plot mode." [INFO] [stdout] 477 | | )] [INFO] [stdout] 478 | | sample: Vec, [INFO] [stdout] | |___________________________^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error: this type will no longer be must used: std::result::Result [INFO] [stdout] --> src/cli.rs:510:9 [INFO] [stdout] | [INFO] [stdout] 510 | / #[structopt( [INFO] [stdout] 511 | | long = "propagate-info-fields", [INFO] [stdout] 512 | | help = "Additional INFO fields in the input BCF that shall be propagated to the output BCF." [INFO] [stdout] 513 | | )] [INFO] [stdout] 514 | | propagate_info_fields: Vec, [INFO] [stdout] | |__________________________________________^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error: this type will no longer be must used: std::result::Result [INFO] [stdout] --> src/cli.rs:574:9 [INFO] [stdout] | [INFO] [stdout] 574 | / #[structopt( [INFO] [stdout] 575 | | long = "testcase-locus", [INFO] [stdout] 576 | | help = "Create a test case for the given locus. Locus must be given in the form \ [INFO] [stdout] 577 | | CHROM:POS. Alternatively, for single variant VCFs, you can \ [INFO] [stdout] 578 | | specify 'all'." [INFO] [stdout] 579 | | )] [INFO] [stdout] 580 | | testcase_locus: Option, [INFO] [stdout] | |______________________________________^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error: this type will no longer be must used: std::result::Result [INFO] [stdout] --> src/cli.rs:581:9 [INFO] [stdout] | [INFO] [stdout] 581 | / #[structopt( [INFO] [stdout] 582 | | long = "testcase-prefix", [INFO] [stdout] 583 | | help = "Create test case files in the given directory." [INFO] [stdout] 584 | | )] [INFO] [stdout] 585 | | testcase_prefix: Option, [INFO] [stdout] | |_______________________________________^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error: this type will no longer be must used: std::result::Result [INFO] [stdout] --> src/cli.rs:591:9 [INFO] [stdout] | [INFO] [stdout] 591 | / #[structopt( [INFO] [stdout] 592 | | long, [INFO] [stdout] 593 | | short, [INFO] [stdout] 594 | | help = "Output variant calls to given path (in BCF format). If omitted, prints calls to STDOUT." [INFO] [stdout] 595 | | )] [INFO] [stdout] 596 | | output: Option, [INFO] [stdout] | |_______________________________^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error: this type will no longer be must used: std::result::Result [INFO] [stdout] --> src/cli.rs:597:9 [INFO] [stdout] | [INFO] [stdout] 597 | / #[structopt( [INFO] [stdout] 598 | | long = "log-mode", [INFO] [stdout] 599 | | possible_values = &["default", "each-record"], [INFO] [stdout] 600 | | default_value = "default", [INFO] [stdout] ... | [INFO] [stdout] 605 | | #[serde(default = "default_log_mode")] [INFO] [stdout] 606 | | log_mode: String, [INFO] [stdout] | |________________________^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error: this type will no longer be must used: std::result::Result [INFO] [stdout] --> src/cli.rs:692:9 [INFO] [stdout] | [INFO] [stdout] 692 | / ... #[structopt( [INFO] [stdout] 693 | | ... long = "obs", [INFO] [stdout] 694 | | ... required = true, [INFO] [stdout] 695 | | ... help = "BCF file with varlociraptor preprocess results for samples defined in the given scenario (given as samplename=path/to/c... [INFO] [stdout] 696 | | ... )] [INFO] [stdout] 697 | | ... sample_observations: Vec, [INFO] [stdout] | |______________________________________^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error: this type will no longer be must used: std::result::Result [INFO] [stdout] --> src/cli.rs:771:9 [INFO] [stdout] | [INFO] [stdout] 771 | / #[structopt(long, help = "Events to consider.")] [INFO] [stdout] 772 | | events: Vec, [INFO] [stdout] | |___________________________^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error: this type will no longer be must used: std::result::Result [INFO] [stdout] --> src/cli.rs:792:9 [INFO] [stdout] | [INFO] [stdout] 792 | / #[structopt(long, help = "Events to consider.")] [INFO] [stdout] 793 | | events: Vec, [INFO] [stdout] | |___________________________^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error: this type will no longer be must used: std::result::Result [INFO] [stdout] --> src/testcase/runner/common/version0.rs:188:13 [INFO] [stdout] | [INFO] [stdout] 188 | / #[structopt( [INFO] [stdout] 189 | | long = "somatic-tumor-events", [INFO] [stdout] 190 | | default_value = "SOMATIC_TUMOR", [INFO] [stdout] 191 | | help = "Events to consider (e.g. SOMATIC_TUMOR)." [INFO] [stdout] 192 | | )] [INFO] [stdout] 193 | | somatic_tumor_events: Vec, [INFO] [stdout] | |_____________________________________________^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error: this type will no longer be must used: std::result::Result [INFO] [stdout] --> src/testcase/runner/common/version0.rs:194:13 [INFO] [stdout] | [INFO] [stdout] 194 | / #[structopt( [INFO] [stdout] 195 | | long = "tumor-sample", [INFO] [stdout] 196 | | default_value = "tumor", [INFO] [stdout] 197 | | help = "Name of the tumor sample in the given VCF/BCF." [INFO] [stdout] 198 | | )] [INFO] [stdout] 199 | | tumor_sample: String, [INFO] [stdout] | |________________________________^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error: this type will no longer be must used: std::result::Result [INFO] [stdout] --> src/testcase/runner/common/version0.rs:286:13 [INFO] [stdout] | [INFO] [stdout] 286 | / #[structopt( [INFO] [stdout] 287 | | long = "testcase-locus", [INFO] [stdout] 288 | | help = "Create a test case for the given locus. Locus must be given in the form \ [INFO] [stdout] 289 | | CHROM:POS[:IDX]. IDX is thereby an optional value to select a particular \ [INFO] [stdout] ... | [INFO] [stdout] 293 | | )] [INFO] [stdout] 294 | | testcase_locus: Option, [INFO] [stdout] | |__________________________________________^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error: this type will no longer be must used: std::result::Result [INFO] [stdout] --> src/testcase/runner/common/version0.rs:295:13 [INFO] [stdout] | [INFO] [stdout] 295 | / #[structopt( [INFO] [stdout] 296 | | long = "testcase-prefix", [INFO] [stdout] 297 | | help = "Create test case files in the given directory." [INFO] [stdout] 298 | | )] [INFO] [stdout] 299 | | testcase_prefix: Option, [INFO] [stdout] | |___________________________________________^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error: this type will no longer be must used: std::result::Result [INFO] [stdout] --> src/testcase/runner/common/version0.rs:388:13 [INFO] [stdout] | [INFO] [stdout] 388 | / #[structopt(long, help = "BAM files with aligned reads for each sample.")] [INFO] [stdout] 389 | | bams: Vec, [INFO] [stdout] | |_____________________________^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error: this type will no longer be must used: std::result::Result [INFO] [stdout] --> src/testcase/runner/common/version0.rs:390:13 [INFO] [stdout] | [INFO] [stdout] 390 | / #[structopt( [INFO] [stdout] 391 | | long = "alignment-properties", [INFO] [stdout] 392 | | help = "Alignment properties JSON file for normal sample. If not provided, properties \ [INFO] [stdout] 393 | | will be estimated from the given BAM file." [INFO] [stdout] 394 | | )] [INFO] [stdout] 395 | | alignment_properties: Vec, [INFO] [stdout] | |_____________________________________________^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error: this type will no longer be must used: std::result::Result [INFO] [stdout] --> src/testcase/runner/common/version0.rs:419:13 [INFO] [stdout] | [INFO] [stdout] 419 | / #[structopt(long, help = "Events to consider.")] [INFO] [stdout] 420 | | events: Vec, [INFO] [stdout] | |_______________________________^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error: this type will no longer be must used: std::result::Result [INFO] [stdout] --> src/testcase/runner/common/version0.rs:439:13 [INFO] [stdout] | [INFO] [stdout] 439 | / #[structopt(long, help = "Events to consider.")] [INFO] [stdout] 440 | | events: Vec, [INFO] [stdout] | |_______________________________^ [INFO] [stdout] [INFO] [stdout] [INFO] [stderr] error: could not compile `varlociraptor` (lib) due to 35 previous errors [INFO] running `Command { std: "docker" "inspect" "e3f7c27fdbee7797475ec71c0c21051cb1e22df33da6d022d1ce44c86d1f2be3", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "e3f7c27fdbee7797475ec71c0c21051cb1e22df33da6d022d1ce44c86d1f2be3", kill_on_drop: false }` [INFO] [stdout] e3f7c27fdbee7797475ec71c0c21051cb1e22df33da6d022d1ce44c86d1f2be3