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Maintainer: y...@freebsd.org Log URL: https://pkg-status.freebsd.org/ampere2/data/main-armv7-default/p71b167230419_s46a9fb7287/logs/coverm-0.7.0_3.log Build URL: https://pkg-status.freebsd.org/ampere2/build.html?mastername=main-armv7-default&build=p71b167230419_s46a9fb7287 Log: =>> Building biology/coverm build started at Wed Jan 29 17:58:12 UTC 2025 port directory: /usr/ports/biology/coverm package name: coverm-0.7.0_3 building for: FreeBSD main-armv7-default-job-05 15.0-CURRENT FreeBSD 15.0-CURRENT 1500030 arm maintained by: y...@freebsd.org Makefile datestamp: -rw-r--r-- 1 root wheel 5806 Jan 25 01:02 /usr/ports/biology/coverm/Makefile Ports top last git commit: 71b16723041 Ports top unclean checkout: no Port dir last git commit: fccaa1b3263 Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.2 Host OSVERSION: 1500028 Jail OSVERSION: 1500030 Job Id: 05 !!! Jail is newer than host. (Jail: 1500030, Host: 1500028) !!! !!! This is not supported. !!! !!! Host kernel must be same or newer than jail. !!! !!! Expect build failures. !!! ---Begin Environment--- SHELL=/bin/sh OSVERSION=1500030 UNAME_v=FreeBSD 15.0-CURRENT 1500030 UNAME_r=15.0-CURRENT BLOCKSIZE=K MAIL=/var/mail/root MM_CHARSET=UTF-8 LANG=C.UTF-8 STATUS=1 HOME=/root PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin MAKE_OBJDIR_CHECK_WRITABLE=0 LOCALBASE=/usr/local USER=root POUDRIERE_NAME=poudriere-git LIBEXECPREFIX=/usr/local/libexec/poudriere POUDRIERE_VERSION=3.4.2 MASTERMNT=/usr/local/poudriere/data/.m/main-armv7-default/ref LC_COLLATE=C POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM= OUTPUT_REDIRECTED_STDERR=4 OUTPUT_REDIRECTED=1 PWD=/usr/local/poudriere/data/.m/main-armv7-default/05/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS MASTERNAME=main-armv7-default SCRIPTPREFIX=/usr/local/share/poudriere SCRIPTNAME=bulk.sh OLDPWD=/usr/local/poudriere/data/.m/main-armv7-default/ref/.p/pool POUDRIERE_PKGNAME=poudriere-git-3.4.2 SCRIPTPATH=/usr/local/share/poudriere/bulk.sh POUDRIEREPATH=/usr/local/bin/poudriere ---End Environment--- ---Begin Poudriere Port Flags/Env--- PORT_FLAGS= PKGENV= FLAVOR= MAKE_ARGS= ---End Poudriere Port Flags/Env--- ---Begin OPTIONS List--- ---End OPTIONS List--- --MAINTAINER-- y...@freebsd.org --End MAINTAINER-- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- PKG_CONFIG=pkgconf XDG_DATA_HOME=/wrkdirs/usr/ports/biology/coverm/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/coverm/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/coverm/work/.cache HOME=/wrkdirs/usr/ports/biology/coverm/work TMPDIR="/wrkdirs/usr/ports/biology/coverm/work" PATH=/wrkdirs/usr/ports/biology/coverm/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/coverm/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig SHELL=/bin/sh CONFIG_SHELL=/bin/sh --End CONFIGURE_ENV-- --MAKE_ENV-- XDG_DATA_HOME=/wrkdirs/usr/ports/biology/coverm/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/coverm/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/coverm/work/.cache HOME=/wrkdirs/usr/ports/biology/coverm/work TMPDIR="/wrkdirs/usr/ports/biology/coverm/work" PATH=/wrkdirs/usr/ports/biology/coverm/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/coverm/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES PREFIX=/usr/local LOCALBASE=/usr/local CC="cc" CFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " CPP="cpp" CPPFLAGS="" LDFLAGS=" -fstack-protector-strong " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " BSD_INSTALL_PROGRAM="install -s -m 555" BSD_INSTALL_LIB="install -s -m 0644" BSD_INSTALL_SCRIPT="install -m 555" BSD_INST ALL_DATA="install -m 0644" BSD_INSTALL_MAN="install -m 444" --End MAKE_ENV-- --PLIST_SUB-- OSREL=15.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/coverm" EXAMPLESDIR="share/examples/coverm" DATADIR="share/coverm" WWWDIR="www/coverm" ETCDIR="etc/coverm" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/coverm DOCSDIR=/usr/local/share/doc/coverm EXAMPLESDIR=/usr/local/share/examples/coverm WWWDIR=/usr/local/www/coverm ETCDIR=/usr/local/etc/coverm --End SUB_LIST-- ---Begin make.conf--- # XXX: We really need this but cannot use it while 'make checksum' does not # try the next mirror on checksum failure. It currently retries the same # failed mirror and then fails rather then trying another. It *does* # try the next if the size is mismatched though. #MASTER_SITE_FREEBSD=yes # Build ALLOW_MAKE_JOBS_PACKAGES with 3 jobs MAKE_JOBS_NUMBER=3 USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles PACKAGE_BUILDING=yes PACKAGE_BUILDING_FLAVORS=yes #### #### # XXX: We really need this but cannot use it while 'make checksum' does not # try the next mirror on checksum failure. It currently retries the same # failed mirror and then fails rather then trying another. It *does* # try the next if the size is mismatched though. #MASTER_SITE_FREEBSD=yes # Build ALLOW_MAKE_JOBS_PACKAGES with 3 jobs MAKE_JOBS_NUMBER=3 #### Misc Poudriere #### .include "/etc/make.conf.ports_env" GID=0 UID=0 ---End make.conf--- --Resource limits-- cpu time (seconds, -t) unlimited file size (512-blocks, -f) unlimited data seg size (kbytes, -d) 524288 stack size (kbytes, -s) 65536 core file size (512-blocks, -c) unlimited max memory size (kbytes, -m) unlimited locked memory (kbytes, -l) unlimited max user processes (-u) 89999 open files (-n) 8192 virtual mem size (kbytes, -v) unlimited swap limit (kbytes, -w) unlimited socket buffer size (bytes, -b) unlimited pseudo-terminals (-p) unlimited kqueues (-k) unlimited umtx shared locks (-o) unlimited pipebuf (-y) unlimited --End resource limits-- =======================<phase: check-sanity >============================ ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> License AGPLv3 accepted by the user =========================================================================== =======================<phase: pkg-depends >============================ ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> coverm-0.7.0_3 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-2.0.3.pkg [main-armv7-default-job-05] Installing pkg-2.0.3... [main-armv7-default-job-05] Extracting pkg-2.0.3: .......... done ===> coverm-0.7.0_3 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of coverm-0.7.0_3 =========================================================================== =======================<phase: fetch-depends >============================ ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =======================<phase: fetch >============================ ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> License AGPLv3 accepted by the user ===> Fetching all distfiles required by coverm-0.7.0_3 for building =========================================================================== =======================<phase: checksum >============================ ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> License AGPLv3 accepted by the user ===> Fetching all distfiles required by coverm-0.7.0_3 for building => SHA256 Checksum OK for rust/crates/addr2line-0.24.2.crate. => SHA256 Checksum OK for rust/crates/adler2-2.0.0.crate. => SHA256 Checksum OK for rust/crates/aho-corasick-1.1.3.crate. => SHA256 Checksum OK for rust/crates/ansi_term-0.12.1.crate. => SHA256 Checksum OK for rust/crates/anstream-0.6.15.crate. => SHA256 Checksum OK for rust/crates/anstyle-1.0.8.crate. => SHA256 Checksum OK for rust/crates/anstyle-parse-0.2.5.crate. => SHA256 Checksum OK for rust/crates/anstyle-query-1.1.1.crate. => SHA256 Checksum OK for rust/crates/anstyle-wincon-3.0.4.crate. => SHA256 Checksum OK for rust/crates/anyhow-1.0.89.crate. => SHA256 Checksum OK for rust/crates/approx-0.5.1.crate. => SHA256 Checksum OK for rust/crates/assert_cli-0.6.3.crate. => SHA256 Checksum OK for rust/crates/atty-0.2.14.crate. => SHA256 Checksum OK for rust/crates/autocfg-1.4.0.crate. => SHA256 Checksum OK for rust/crates/backtrace-0.3.74.crate. => SHA256 Checksum OK for rust/crates/bincode-1.3.3.crate. => SHA256 Checksum OK for rust/crates/bio-1.6.0.crate. => SHA256 Checksum OK for rust/crates/bio-types-1.0.4.crate. => SHA256 Checksum OK for rust/crates/bird_tool_utils-0.5.1.crate. => SHA256 Checksum OK for rust/crates/bird_tool_utils-man-0.4.0.crate. => SHA256 Checksum OK for rust/crates/bit-set-0.5.3.crate. => SHA256 Checksum OK for rust/crates/bit-vec-0.5.1.crate. => SHA256 Checksum OK for rust/crates/bit-vec-0.6.3.crate. => SHA256 Checksum OK for rust/crates/bitflags-1.3.2.crate. => SHA256 Checksum OK for rust/crates/bitflags-2.6.0.crate. => SHA256 Checksum OK for rust/crates/buf_redux-0.8.4.crate. => SHA256 Checksum OK for rust/crates/buffer-redux-1.0.2.crate. => SHA256 Checksum OK for rust/crates/bv-0.11.1.crate. => SHA256 Checksum OK for rust/crates/bytecount-0.6.8.crate. => SHA256 Checksum OK for rust/crates/bytemuck-1.18.0.crate. <snip> [hts-sys 2.1.4] cargo:rerun-if-env-changed=ARFLAGS [hts-sys 2.1.4] ARFLAGS = None [hts-sys 2.1.4] cargo:rustc-link-lib=static=hts [hts-sys 2.1.4] cargo:rustc-link-search=native=/wrkdirs/usr/ports/biology/coverm/work/target/release/build/hts-sys-060f8b17d90a2ce0/out [hts-sys 2.1.4] cargo:rerun-if-changed=linux_prebuilt_bindings.rs [hts-sys 2.1.4] cargo:root=/wrkdirs/usr/ports/biology/coverm/work/target/release/build/hts-sys-060f8b17d90a2ce0/out [hts-sys 2.1.4] cargo:include=/wrkdirs/usr/ports/biology/coverm/work/target/release/build/hts-sys-060f8b17d90a2ce0/out/include [hts-sys 2.1.4] cargo:libdir=/wrkdirs/usr/ports/biology/coverm/work/target/release/build/hts-sys-060f8b17d90a2ce0/out [hts-sys 2.1.4] cargo:rerun-if-changed=wrapper.c [hts-sys 2.1.4] cargo:rerun-if-changed=wrapper.h [hts-sys 2.1.4] cargo:rerun-if-changed=htslib/bcf_sr_sort.h [hts-sys 2.1.4] cargo:rerun-if-changed=htslib/fuzz_settings.h [hts-sys 2.1.4] cargo:rerun-if-changed=htslib/header.h [hts-sys 2.1.4] cargo:rerun-if-changed=htslib/hfile_internal.h [hts-sys 2.1.4] cargo:rerun-if-changed=htslib/hts_internal.h [hts-sys 2.1.4] cargo:rerun-if-changed=htslib/hts_time_funcs.h [hts-sys 2.1.4] cargo:rerun-if-changed=htslib/sam_internal.h [hts-sys 2.1.4] cargo:rerun-if-changed=htslib/textutils_internal.h [hts-sys 2.1.4] cargo:rerun-if-changed=htslib/thread_pool_internal.h [hts-sys 2.1.4] cargo:rerun-if-changed=htslib/cram/cram.h [hts-sys 2.1.4] cargo:rerun-if-changed=htslib/cram/cram_codecs.h [hts-sys 2.1.4] cargo:rerun-if-changed=htslib/cram/cram_decode.h [hts-sys 2.1.4] cargo:rerun-if-changed=htslib/cram/cram_encode.h [hts-sys 2.1.4] cargo:rerun-if-changed=htslib/cram/cram_index.h [hts-sys 2.1.4] cargo:rerun-if-changed=htslib/cram/cram_io.h [hts-sys 2.1.4] cargo:rerun-if-changed=htslib/cram/cram_samtools.h [hts-sys 2.1.4] cargo:rerun-if-changed=htslib/cram/cram_stats.h [hts-sys 2.1.4] cargo:rerun-if-changed=htslib/cram/cram_structs.h [hts-sys 2.1.4] cargo:rerun-if-changed=htslib/cram/mFILE.h [hts-sys 2.1.4] cargo:rerun-if-changed=htslib/cram/misc.h [hts-sys 2.1.4] cargo:rerun-if-changed=htslib/cram/open_trace_file.h [hts-sys 2.1.4] cargo:rerun-if-changed=htslib/cram/os.h [hts-sys 2.1.4] cargo:rerun-if-changed=htslib/cram/pooled_alloc.h [hts-sys 2.1.4] cargo:rerun-if-changed=htslib/cram/string_alloc.h [hts-sys 2.1.4] cargo:rerun-if-changed=htslib/htslib/bgzf.h [hts-sys 2.1.4] cargo:rerun-if-changed=htslib/htslib/cram.h [hts-sys 2.1.4] cargo:rerun-if-changed=htslib/htslib/faidx.h [hts-sys 2.1.4] cargo:rerun-if-changed=htslib/htslib/hfile.h [hts-sys 2.1.4] cargo:rerun-if-changed=htslib/htslib/hts.h [hts-sys 2.1.4] cargo:rerun-if-changed=htslib/htslib/hts_defs.h [hts-sys 2.1.4] cargo:rerun-if-changed=htslib/htslib/hts_endian.h [hts-sys 2.1.4] cargo:rerun-if-changed=htslib/htslib/hts_expr.h [hts-sys 2.1.4] cargo:rerun-if-changed=htslib/htslib/hts_log.h [hts-sys 2.1.4] cargo:rerun-if-changed=htslib/htslib/hts_os.h [hts-sys 2.1.4] cargo:rerun-if-changed=htslib/htslib/kbitset.h [hts-sys 2.1.4] cargo:rerun-if-changed=htslib/htslib/kfunc.h [hts-sys 2.1.4] cargo:rerun-if-changed=htslib/htslib/khash.h [hts-sys 2.1.4] cargo:rerun-if-changed=htslib/htslib/khash_str2int.h [hts-sys 2.1.4] cargo:rerun-if-changed=htslib/htslib/klist.h [hts-sys 2.1.4] cargo:rerun-if-changed=htslib/htslib/knetfile.h [hts-sys 2.1.4] cargo:rerun-if-changed=htslib/htslib/kroundup.h [hts-sys 2.1.4] cargo:rerun-if-changed=htslib/htslib/kseq.h [hts-sys 2.1.4] cargo:rerun-if-changed=htslib/htslib/ksort.h [hts-sys 2.1.4] cargo:rerun-if-changed=htslib/htslib/kstring.h [hts-sys 2.1.4] cargo:rerun-if-changed=htslib/htslib/regidx.h [hts-sys 2.1.4] cargo:rerun-if-changed=htslib/htslib/sam.h [hts-sys 2.1.4] cargo:rerun-if-changed=htslib/htslib/synced_bcf_reader.h [hts-sys 2.1.4] cargo:rerun-if-changed=htslib/htslib/tbx.h [hts-sys 2.1.4] cargo:rerun-if-changed=htslib/htslib/thread_pool.h [hts-sys 2.1.4] cargo:rerun-if-changed=htslib/htslib/vcf.h [hts-sys 2.1.4] cargo:rerun-if-changed=htslib/htslib/vcf_sweep.h [hts-sys 2.1.4] cargo:rerun-if-changed=htslib/htslib/vcfutils.h [hts-sys 2.1.4] cargo:rerun-if-changed=htslib/os/lzma_stub.h Running `CARGO=/usr/local/bin/cargo CARGO_CRATE_NAME=hts_sys CARGO_MANIFEST_DIR=/wrkdirs/usr/ports/biology/coverm/work/CoverM-0.7.0/cargo-crates/hts-sys-2.1.4 CARGO_MANIFEST_PATH=/wrkdirs/usr/ports/biology/coverm/work/CoverM-0.7.0/cargo-crates/hts-sys-2.1.4/Cargo.toml CARGO_PKG_AUTHORS='Christopher Schröder <christopher.schroe...@tu-dortmund.de>:Johannes Köster <johannes.koes...@tu-dortmund.de>' CARGO_PKG_DESCRIPTION='This library provides HTSlib bindings.' CARGO_PKG_HOMEPAGE='' CARGO_PKG_LICENSE=MIT CARGO_PKG_LICENSE_FILE='' CARGO_PKG_NAME=hts-sys CARGO_PKG_README=README.md CARGO_PKG_REPOSITORY='https://github.com/samtools/htslib.git' CARGO_PKG_RUST_VERSION='' CARGO_PKG_VERSION=2.1.4 CARGO_PKG_VERSION_MAJOR=2 CARGO_PKG_VERSION_MINOR=1 CARGO_PKG_VERSION_PATCH=4 CARGO_PKG_VERSION_PRE='' LD_LIBRARY_PATH=/wrkdirs/usr/ports/biology/coverm/work/target/release/deps OUT_DIR=/wrkdirs/usr/ports/biology/coverm/work/target/release/build/hts-sys-060f8b17d90a2ce0/out /usr/local/bi n/rustc --crate-name hts_sys --edition=2018 /wrkdirs/usr/ports/biology/coverm/work/CoverM-0.7.0/cargo-crates/hts-sys-2.1.4/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C panic=abort -C linker-plugin-lto -C codegen-units=1 --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values("bindgen", "bzip2", "bzip2-sys", "curl", "curl-sys", "default", "gcs", "libdeflate", "libdeflate-sys", "lzma", "lzma-sys", "openssl-sys", "s3", "static"))' -C metadata=823437032b6870bf -C extra-filename=-823437032b6870bf --out-dir /wrkdirs/usr/ports/biology/coverm/work/target/release/deps -C strip=symbols -L dependency=/wrkdirs/usr/ports/biology/coverm/work/target/release/deps --extern libz_sys=/wrkdirs/usr/ports/biology/coverm/work/target/release/deps/liblibz_sys-1c7f2ad71c312c58.rmeta --cap-lints warn -C target-cpu= -C link-arg=-fstack-protector-strong -L native=/wrkdirs/usr/ports/biology/cov erm/work/target/release/build/hts-sys-060f8b17d90a2ce0/out -l static=hts -L native=/wrkdirs/usr/ports/biology/coverm/work/target/release/build/libz-sys-2def2a3f061361a7/out/lib -L native=/wrkdirs/usr/ports/biology/coverm/work/target/release/build/libz-sys-2def2a3f061361a7/out/lib64` warning: `nix` (lib) generated 10 warnings Compiling clap_complete v4.5.32 Running `CARGO=/usr/local/bin/cargo CARGO_CRATE_NAME=clap_complete CARGO_MANIFEST_DIR=/wrkdirs/usr/ports/biology/coverm/work/CoverM-0.7.0/cargo-crates/clap_complete-4.5.32 CARGO_MANIFEST_PATH=/wrkdirs/usr/ports/biology/coverm/work/CoverM-0.7.0/cargo-crates/clap_complete-4.5.32/Cargo.toml CARGO_PKG_AUTHORS='' CARGO_PKG_DESCRIPTION='Generate shell completion scripts for your clap::Command' CARGO_PKG_HOMEPAGE='' CARGO_PKG_LICENSE='MIT OR Apache-2.0' CARGO_PKG_LICENSE_FILE='' CARGO_PKG_NAME=clap_complete CARGO_PKG_README=README.md CARGO_PKG_REPOSITORY='https://github.com/clap-rs/clap' CARGO_PKG_RUST_VERSION=1.74 CARGO_PKG_VERSION=4.5.32 CARGO_PKG_VERSION_MAJOR=4 CARGO_PKG_VERSION_MINOR=5 CARGO_PKG_VERSION_PATCH=32 CARGO_PKG_VERSION_PRE='' LD_LIBRARY_PATH=/wrkdirs/usr/ports/biology/coverm/work/target/release/deps /usr/local/bin/rustc --crate-name clap_complete --edition=2021 /wrkdirs/usr/ports/biology/coverm/work/CoverM-0.7.0/cargo-crates/clap_complete-4.5.32/src/lib.rs --er ror-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C panic=abort -C linker-plugin-lto -C codegen-units=1 --warn=rust_2018_idioms '--warn=clippy::zero_sized_map_values' '--warn=clippy::verbose_file_reads' --warn=unused_qualifications --warn=unused_macro_rules --warn=unused_lifetimes --warn=unsafe_op_in_unsafe_fn --warn=unreachable_pub '--warn=clippy::uninlined_format_args' '--warn=clippy::trait_duplication_in_bounds' '--warn=clippy::todo' '--warn=clippy::string_lit_as_bytes' '--warn=clippy::string_add_assign' '--warn=clippy::semicolon_if_nothing_returned' '--warn=clippy::self_named_module_files' '--warn=clippy::same_functions_in_if_condition' '--warn=clippy::rest_pat_in_fully_bound_structs' '--warn=clippy::ref_option_ref' '--warn=clippy::redundant_feature_names' '--warn=clippy::rc_mutex' '--warn=clippy::ptr_as_ptr' '--warn=clippy::path_buf_push_overwrite' '--warn=clippy::negative_feature_nam es' '--warn=clippy::needless_for_each' '--warn=clippy::needless_continue' '--warn=clippy::mutex_integer' '--allow=clippy::multiple_bound_locations' '--warn=clippy::mem_forget' '--warn=clippy::macro_use_imports' '--warn=clippy::lossy_float_literal' '--warn=clippy::linkedlist' '--allow=clippy::let_and_return' '--warn=clippy::large_types_passed_by_value' '--warn=clippy::large_stack_arrays' '--warn=clippy::large_digit_groups' '--warn=clippy::invalid_upcast_comparisons' '--warn=clippy::infinite_loop' '--warn=clippy::inefficient_to_string' '--warn=clippy::inconsistent_struct_constructor' '--warn=clippy::imprecise_flops' '--warn=clippy::implicit_clone' '--allow=clippy::if_same_then_else' '--warn=clippy::from_iter_instead_of_collect' '--warn=clippy::fn_params_excessive_bools' '--warn=clippy::float_cmp_const' '--warn=clippy::flat_map_option' '--warn=clippy::filter_map_next' '--warn=clippy::fallible_impl_from' '--warn=clippy::explicit_into_iter_loop' '--warn=clippy::explicit_deref_met hods' '--warn=clippy::expl_impl_clone_on_copy' '--warn=clippy::enum_glob_use' '--warn=clippy::empty_enum' '--warn=clippy::doc_markdown' '--warn=clippy::debug_assert_with_mut_call' '--warn=clippy::dbg_macro' '--warn=clippy::create_dir' '--allow=clippy::collapsible_else_if' '--warn=clippy::checked_conversions' '--allow=clippy::branches_sharing_code' '--allow=clippy::bool_assert_comparison' '--allow=clippy::blocks_in_conditions' '--allow=clippy::assigning_clones' --cfg 'feature="default"' --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values("debug", "default", "unstable-doc", "unstable-dynamic", "unstable-shell-tests"))' -C metadata=42fa876b6c1d2c05 -C extra-filename=-42fa876b6c1d2c05 --out-dir /wrkdirs/usr/ports/biology/coverm/work/target/release/deps -C strip=symbols -L dependency=/wrkdirs/usr/ports/biology/coverm/work/target/release/deps --extern clap=/wrkdirs/usr/ports/biology/coverm/work/target/release/deps/libclap-89934ce1fda35ad3.rmeta --cap-lints warn -C target-cp u= -C link-arg=-fstack-protector-strong` Compiling rust-htslib v0.44.1 Running `CARGO=/usr/local/bin/cargo CARGO_CRATE_NAME=rust_htslib CARGO_MANIFEST_DIR=/wrkdirs/usr/ports/biology/coverm/work/CoverM-0.7.0/cargo-crates/rust-htslib-0.44.1 CARGO_MANIFEST_PATH=/wrkdirs/usr/ports/biology/coverm/work/CoverM-0.7.0/cargo-crates/rust-htslib-0.44.1/Cargo.toml CARGO_PKG_AUTHORS='Christopher Schröder <christopher.schroe...@tu-dortmund.de>:Johannes Köster <johannes.koes...@tu-dortmund.de>' CARGO_PKG_DESCRIPTION='This library provides HTSlib bindings and a high level Rust API for reading and writing BAM files.' CARGO_PKG_HOMEPAGE='' CARGO_PKG_LICENSE=MIT CARGO_PKG_LICENSE_FILE='' CARGO_PKG_NAME=rust-htslib CARGO_PKG_README=README.md CARGO_PKG_REPOSITORY='https://github.com/rust-bio/rust-htslib.git' CARGO_PKG_RUST_VERSION='' CARGO_PKG_VERSION=0.44.1 CARGO_PKG_VERSION_MAJOR=0 CARGO_PKG_VERSION_MINOR=44 CARGO_PKG_VERSION_PATCH=1 CARGO_PKG_VERSION_PRE='' LD_LIBRARY_PATH=/wrkdirs/usr/ports/biology/coverm/work/target/release/deps /usr/local/bin/rustc --cr ate-name rust_htslib --edition=2018 /wrkdirs/usr/ports/biology/coverm/work/CoverM-0.7.0/cargo-crates/rust-htslib-0.44.1/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C panic=abort -C linker-plugin-lto -C codegen-units=1 --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values("bindgen", "bzip2", "curl", "default", "gcs", "libdeflate", "lzma", "s3", "serde", "serde_bytes", "serde_feature", "static"))' -C metadata=2e1e2ec566e740d8 -C extra-filename=-2e1e2ec566e740d8 --out-dir /wrkdirs/usr/ports/biology/coverm/work/target/release/deps -C strip=symbols -L dependency=/wrkdirs/usr/ports/biology/coverm/work/target/release/deps --extern bio_types=/wrkdirs/usr/ports/biology/coverm/work/target/release/deps/libbio_types-6f1d69865a722342.rmeta --extern byteorder=/wrkdirs/usr/ports/biology/coverm/work/target/release/deps/libbyteorder-b4b9c9872cae6271.rmeta --extern custom_derive=/w rkdirs/usr/ports/biology/coverm/work/target/release/deps/libcustom_derive-4d9ae09796cc0627.rmeta --extern derive_new=/wrkdirs/usr/ports/biology/coverm/work/target/release/deps/libderive_new-76c5daafb43cad04.so --extern hts_sys=/wrkdirs/usr/ports/biology/coverm/work/target/release/deps/libhts_sys-823437032b6870bf.rmeta --extern ieee754=/wrkdirs/usr/ports/biology/coverm/work/target/release/deps/libieee754-2c3d8632817e427b.rmeta --extern lazy_static=/wrkdirs/usr/ports/biology/coverm/work/target/release/deps/liblazy_static-7feea6c76f34b6ae.rmeta --extern libc=/wrkdirs/usr/ports/biology/coverm/work/target/release/deps/liblibc-8af20619584b5e91.rmeta --extern linear_map=/wrkdirs/usr/ports/biology/coverm/work/target/release/deps/liblinear_map-4e14052681698b40.rmeta --extern newtype_derive=/wrkdirs/usr/ports/biology/coverm/work/target/release/deps/libnewtype_derive-4db681354db23ac7.rmeta --extern regex=/wrkdirs/usr/ports/biology/coverm/work/target/release/deps/libregex-b4d629d1d01b0f 13.rmeta --extern thiserror=/wrkdirs/usr/ports/biology/coverm/work/target/release/deps/libthiserror-9f1e5c92660c7112.rmeta --extern url=/wrkdirs/usr/ports/biology/coverm/work/target/release/deps/liburl-5247e8c94ef89b2e.rmeta --cap-lints warn -C target-cpu= -C link-arg=-fstack-protector-strong -L native=/wrkdirs/usr/ports/biology/coverm/work/target/release/build/hts-sys-060f8b17d90a2ce0/out -L native=/wrkdirs/usr/ports/biology/coverm/work/target/release/build/libz-sys-2def2a3f061361a7/out/lib -L native=/wrkdirs/usr/ports/biology/coverm/work/target/release/build/libz-sys-2def2a3f061361a7/out/lib64` error[E0308]: mismatched types --> /wrkdirs/usr/ports/biology/coverm/work/CoverM-0.7.0/cargo-crates/rust-htslib-0.44.1/src/bam/record.rs:154:16 | 154 | l: sam_copy.len() as u64, | ^^^^^^^^^^^^^^^^^^^^^ expected `u32`, found `u64` error[E0308]: mismatched types --> /wrkdirs/usr/ports/biology/coverm/work/CoverM-0.7.0/cargo-crates/rust-htslib-0.44.1/src/bam/record.rs:155:16 | 155 | m: sam_copy.len() as u64, | ^^^^^^^^^^^^^^^^^^^^^ expected `u32`, found `u64` error[E0308]: mismatched types --> /wrkdirs/usr/ports/biology/coverm/work/CoverM-0.7.0/cargo-crates/rust-htslib-0.44.1/src/bam/mod.rs:179:21 | 177 | i64::from(htslib::cram_seek( | ----------------- arguments to this function are incorrect 178 | htsfile.fp.cram, 179 | offset as libc::off_t, | ^^^^^^^^^^^^^^^^^^^^^ expected `i32`, found `i64` | note: function defined here --> /wrkdirs/usr/ports/biology/coverm/work/target/release/build/hts-sys-060f8b17d90a2ce0/out/bindings.rs:9704:12 | 9704 | pub fn cram_seek( | ^^^^^^^^^ help: you can convert an `i64` to an `i32` and panic if the converted value doesn't fit | 179 | (offset as libc::off_t).try_into().unwrap(), | + +++++++++++++++++++++ error[E0308]: mismatched types --> /wrkdirs/usr/ports/biology/coverm/work/CoverM-0.7.0/cargo-crates/rust-htslib-0.44.1/src/bam/mod.rs:1128:29 | 1128 | (*rec).l_text = l_text as u64; | ------------- ^^^^^^^^^^^^^ expected `u32`, found `u64` | | | expected due to the type of this binding error[E0308]: mismatched types --> /wrkdirs/usr/ports/biology/coverm/work/CoverM-0.7.0/cargo-crates/rust-htslib-0.44.1/src/bam/mod.rs:1393:45 | 1393 | let rec = htslib::sam_hdr_parse((l_text + 1) as u64, text as *const c_char); | --------------------- ^^^^^^^^^^^^^^^^^^^ expected `u32`, found `u64` | | | arguments to this function are incorrect | note: function defined here --> /wrkdirs/usr/ports/biology/coverm/work/target/release/build/hts-sys-060f8b17d90a2ce0/out/bindings.rs:8520:12 | 8520 | pub fn sam_hdr_parse(l_text: size_t, text: *const ::std::os::raw::c_char) -> *mut sam_hdr_t; | ^^^^^^^^^^^^^ help: you can convert a `u64` to a `u32` and panic if the converted value doesn't fit | 1393 | let rec = htslib::sam_hdr_parse(((l_text + 1) as u64).try_into().unwrap(), text as *const c_char); | + +++++++++++++++++++++ error[E0308]: mismatched types --> /wrkdirs/usr/ports/biology/coverm/work/CoverM-0.7.0/cargo-crates/rust-htslib-0.44.1/src/bam/mod.rs:1395:29 | 1395 | (*rec).l_text = l_text as u64; | ------------- ^^^^^^^^^^^^^ expected `u32`, found `u64` | | | expected due to the type of this binding error[E0308]: mismatched types --> /wrkdirs/usr/ports/biology/coverm/work/CoverM-0.7.0/cargo-crates/rust-htslib-0.44.1/src/bcf/record.rs:1011:48 | 1011 | let rm_set = unsafe { htslib::kbs_init(remove.len() as u64) }; | ---------------- ^^^^^^^^^^^^^^^^^^^ expected `u32`, found `u64` | | | arguments to this function are incorrect | note: function defined here --> /wrkdirs/usr/ports/biology/coverm/work/target/release/build/hts-sys-060f8b17d90a2ce0/out/bindings.rs:11642:12 | 11642 | pub fn kbs_init(ni: size_t) -> *mut kbitset_t; | ^^^^^^^^ help: you can convert a `u64` to a `u32` and panic if the converted value doesn't fit | 1011 | let rm_set = unsafe { htslib::kbs_init((remove.len() as u64).try_into().unwrap()) }; | + +++++++++++++++++++++ error[E0308]: mismatched types --> /wrkdirs/usr/ports/biology/coverm/work/CoverM-0.7.0/cargo-crates/rust-htslib-0.44.1/src/bgzf/mod.rs:118:17 | 115 | htslib::bgzf_read( | ----------------- arguments to this function are incorrect ... 118 | buf.len() as u64, | ^^^^^^^^^^^^^^^^ expected `u32`, found `u64` | note: function defined here --> /wrkdirs/usr/ports/biology/coverm/work/target/release/build/hts-sys-060f8b17d90a2ce0/out/bindings.rs:10097:12 | 10097 | pub fn bgzf_read(fp: *mut BGZF, data: *mut ::std::os::raw::c_void, length: size_t) -> ssize_t; | ^^^^^^^^^ help: you can convert a `u64` to a `u32` and panic if the converted value doesn't fit | 118 | (buf.len() as u64).try_into().unwrap(), | + +++++++++++++++++++++ error[E0308]: mismatched types --> /wrkdirs/usr/ports/biology/coverm/work/CoverM-0.7.0/cargo-crates/rust-htslib-0.44.1/src/bgzf/mod.rs:264:17 | 261 | htslib::bgzf_write( | ------------------ arguments to this function are incorrect ... 264 | buf.len() as u64, | ^^^^^^^^^^^^^^^^ expected `u32`, found `u64` | note: function defined here --> /wrkdirs/usr/ports/biology/coverm/work/target/release/build/hts-sys-060f8b17d90a2ce0/out/bindings.rs:10100:12 | 10100 | pub fn bgzf_write( | ^^^^^^^^^^ help: you can convert a `u64` to a `u32` and panic if the converted value doesn't fit | 264 | (buf.len() as u64).try_into().unwrap(), | + +++++++++++++++++++++ For more information about this error, try `rustc --explain E0308`. error: could not compile `rust-htslib` (lib) due to 9 previous errors Caused by: process didn't exit successfully: `CARGO=/usr/local/bin/cargo CARGO_CRATE_NAME=rust_htslib CARGO_MANIFEST_DIR=/wrkdirs/usr/ports/biology/coverm/work/CoverM-0.7.0/cargo-crates/rust-htslib-0.44.1 CARGO_MANIFEST_PATH=/wrkdirs/usr/ports/biology/coverm/work/CoverM-0.7.0/cargo-crates/rust-htslib-0.44.1/Cargo.toml CARGO_PKG_AUTHORS='Christopher Schröder <christopher.schroe...@tu-dortmund.de>:Johannes Köster <johannes.koes...@tu-dortmund.de>' CARGO_PKG_DESCRIPTION='This library provides HTSlib bindings and a high level Rust API for reading and writing BAM files.' CARGO_PKG_HOMEPAGE='' CARGO_PKG_LICENSE=MIT CARGO_PKG_LICENSE_FILE='' CARGO_PKG_NAME=rust-htslib CARGO_PKG_README=README.md CARGO_PKG_REPOSITORY='https://github.com/rust-bio/rust-htslib.git' CARGO_PKG_RUST_VERSION='' CARGO_PKG_VERSION=0.44.1 CARGO_PKG_VERSION_MAJOR=0 CARGO_PKG_VERSION_MINOR=44 CARGO_PKG_VERSION_PATCH=1 CARGO_PKG_VERSION_PRE='' LD_LIBRARY_PATH=/wrkdirs/usr/ports/biology/coverm/work/target/release/deps /u sr/local/bin/rustc --crate-name rust_htslib --edition=2018 /wrkdirs/usr/ports/biology/coverm/work/CoverM-0.7.0/cargo-crates/rust-htslib-0.44.1/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C panic=abort -C linker-plugin-lto -C codegen-units=1 --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values("bindgen", "bzip2", "curl", "default", "gcs", "libdeflate", "lzma", "s3", "serde", "serde_bytes", "serde_feature", "static"))' -C metadata=2e1e2ec566e740d8 -C extra-filename=-2e1e2ec566e740d8 --out-dir /wrkdirs/usr/ports/biology/coverm/work/target/release/deps -C strip=symbols -L dependency=/wrkdirs/usr/ports/biology/coverm/work/target/release/deps --extern bio_types=/wrkdirs/usr/ports/biology/coverm/work/target/release/deps/libbio_types-6f1d69865a722342.rmeta --extern byteorder=/wrkdirs/usr/ports/biology/coverm/work/target/release/deps/libbyteorder-b4b9c9872cae6271.rmeta -- extern custom_derive=/wrkdirs/usr/ports/biology/coverm/work/target/release/deps/libcustom_derive-4d9ae09796cc0627.rmeta --extern derive_new=/wrkdirs/usr/ports/biology/coverm/work/target/release/deps/libderive_new-76c5daafb43cad04.so --extern hts_sys=/wrkdirs/usr/ports/biology/coverm/work/target/release/deps/libhts_sys-823437032b6870bf.rmeta --extern ieee754=/wrkdirs/usr/ports/biology/coverm/work/target/release/deps/libieee754-2c3d8632817e427b.rmeta --extern lazy_static=/wrkdirs/usr/ports/biology/coverm/work/target/release/deps/liblazy_static-7feea6c76f34b6ae.rmeta --extern libc=/wrkdirs/usr/ports/biology/coverm/work/target/release/deps/liblibc-8af20619584b5e91.rmeta --extern linear_map=/wrkdirs/usr/ports/biology/coverm/work/target/release/deps/liblinear_map-4e14052681698b40.rmeta --extern newtype_derive=/wrkdirs/usr/ports/biology/coverm/work/target/release/deps/libnewtype_derive-4db681354db23ac7.rmeta --extern regex=/wrkdirs/usr/ports/biology/coverm/work/target/release/deps/ libregex-b4d629d1d01b0f13.rmeta --extern thiserror=/wrkdirs/usr/ports/biology/coverm/work/target/release/deps/libthiserror-9f1e5c92660c7112.rmeta --extern url=/wrkdirs/usr/ports/biology/coverm/work/target/release/deps/liburl-5247e8c94ef89b2e.rmeta --cap-lints warn -C target-cpu= -C link-arg=-fstack-protector-strong -L native=/wrkdirs/usr/ports/biology/coverm/work/target/release/build/hts-sys-060f8b17d90a2ce0/out -L native=/wrkdirs/usr/ports/biology/coverm/work/target/release/build/libz-sys-2def2a3f061361a7/out/lib -L native=/wrkdirs/usr/ports/biology/coverm/work/target/release/build/libz-sys-2def2a3f061361a7/out/lib64` (exit status: 1) warning: build failed, waiting for other jobs to finish... *** Error code 101 Stop. make: stopped making "build" in /usr/ports/biology/coverm
