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Maintainer: y...@freebsd.org Log URL: https://pkg-status.freebsd.org/ampere1/data/133arm64-quarterly/b0b3c748c188/logs/coverm-0.7.0.log Build URL: https://pkg-status.freebsd.org/ampere1/build.html?mastername=133arm64-quarterly&build=b0b3c748c188 Log: =>> Building biology/coverm build started at Sun Dec 1 23:27:12 UTC 2024 port directory: /usr/ports/biology/coverm package name: coverm-0.7.0 building for: FreeBSD 133arm64-quarterly-job-04 13.3-RELEASE-p8 FreeBSD 13.3-RELEASE-p8 arm64 maintained by: y...@freebsd.org Makefile datestamp: -rw-r--r-- 1 root wheel 5708 Oct 15 01:02 /usr/ports/biology/coverm/Makefile Ports top last git commit: b0b3c748c Ports top unclean checkout: no Port dir last git commit: db5128afd Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.2 Host OSVERSION: 1500027 Jail OSVERSION: 1303001 Job Id: 04 ---Begin Environment--- SHELL=/bin/csh OSVERSION=1303001 UNAME_v=FreeBSD 13.3-RELEASE-p8 UNAME_r=13.3-RELEASE-p8 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/133arm64-quarterly/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/133arm64-quarterly/04/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS MASTERNAME=133arm64-quarterly SCRIPTPREFIX=/usr/local/share/poudriere SCRIPTNAME=bulk.sh OLDPWD=/usr/local/poudriere/data/.m/133arm64-quarterly/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_INSTA LL_DATA="install -m 0644" BSD_INSTALL_MAN="install -m 444" --End MAKE_ENV-- --PLIST_SUB-- OSREL=13.3 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--- 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) 1048576 stack size (kbytes, -s) 1048576 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 --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 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.21.3.pkg [133arm64-quarterly-job-04] Installing pkg-1.21.3... [133arm64-quarterly-job-04] Extracting pkg-1.21.3: .......... done ===> coverm-0.7.0 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of coverm-0.7.0 =========================================================================== =======================<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 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 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. => SHA256 Checksum OK for rust/crates/byteorder-1.5.0.crate. => SHA256 Checksum OK for rust/crates/bzip2-0.4.4.crate. => SHA256 Checksum OK for rust/crates/bzip2-sys-0.1.11+1.0.8.crate. => SHA256 Checksum OK for rust/crates/capnp-0.14.11.crate. => SHA256 Checksum OK for rust/crates/cargo-husky-1.5.0.crate. => SHA256 Checksum OK for rust/crates/cc-1.1.24.crate. => SHA256 Checksum OK for rust/crates/cfg-if-1.0.0.crate. => SHA256 Checksum OK for rust/crates/checkm-0.2.0.crate. => SHA256 Checksum OK for rust/crates/clap-3.2.25.crate. => SHA256 Checksum OK for rust/crates/clap-4.5.19.crate. => SHA256 Checksum OK for rust/crates/clap_builder-4.5.19.crate. => SHA256 Checksum OK for rust/crates/clap_complete-4.5.32.crate. => SHA256 Checksum OK for rust/crates/clap_lex-0.2.4.crate. => SHA256 Checksum OK for rust/crates/clap_lex-0.7.2.crate. => SHA256 Checksum OK for rust/crates/cmake-0.1.51.crate. => SHA256 Checksum OK for rust/crates/colorchoice-1.0.2.crate. => SHA256 Checksum OK for rust/crates/colored-1.9.4.crate. => SHA256 Checksum OK for rust/crates/concurrent-queue-2.5.0.crate. <snip> | = help: consider using a Cargo feature instead = help: or consider adding in `Cargo.toml` the `check-cfg` lint config for the lint: [lints.rust] unexpected_cfgs = { level = "warn", check-cfg = ['cfg(fbsd14)'] } = help: or consider adding `println!("cargo::rustc-check-cfg=cfg(fbsd14)");` to the top of the `build.rs` = note: see <https://doc.rust-lang.org/nightly/rustc/check-cfg/cargo-specifics.html> for more information about checking conditional configuration warning: unexpected `cfg` condition name: `fbsd14` --> /wrkdirs/usr/ports/biology/coverm/work/CoverM-0.7.0/cargo-crates/nix-0.26.4/src/sys/aio.rs:627:12 | 627 | #[cfg_attr(fbsd14, doc = " ```")] | ^^^^^^ | = help: consider using a Cargo feature instead = help: or consider adding in `Cargo.toml` the `check-cfg` lint config for the lint: [lints.rust] unexpected_cfgs = { level = "warn", check-cfg = ['cfg(fbsd14)'] } = help: or consider adding `println!("cargo::rustc-check-cfg=cfg(fbsd14)");` to the top of the `build.rs` = note: see <https://doc.rust-lang.org/nightly/rustc/check-cfg/cargo-specifics.html> for more information about checking conditional configuration warning: unexpected `cfg` condition name: `fbsd14` --> /wrkdirs/usr/ports/biology/coverm/work/CoverM-0.7.0/cargo-crates/nix-0.26.4/src/sys/aio.rs:628:16 | 628 | #[cfg_attr(not(fbsd14), doc = " ```no_run")] | ^^^^^^ | = help: consider using a Cargo feature instead = help: or consider adding in `Cargo.toml` the `check-cfg` lint config for the lint: [lints.rust] unexpected_cfgs = { level = "warn", check-cfg = ['cfg(fbsd14)'] } = help: or consider adding `println!("cargo::rustc-check-cfg=cfg(fbsd14)");` to the top of the `build.rs` = note: see <https://doc.rust-lang.org/nightly/rustc/check-cfg/cargo-specifics.html> for more information about checking conditional configuration warning: unexpected `cfg` condition name: `fbsd14` --> /wrkdirs/usr/ports/biology/coverm/work/CoverM-0.7.0/cargo-crates/nix-0.26.4/src/sys/aio.rs:862:12 | 862 | #[cfg_attr(fbsd14, doc = " ```")] | ^^^^^^ | = help: consider using a Cargo feature instead = help: or consider adding in `Cargo.toml` the `check-cfg` lint config for the lint: [lints.rust] unexpected_cfgs = { level = "warn", check-cfg = ['cfg(fbsd14)'] } = help: or consider adding `println!("cargo::rustc-check-cfg=cfg(fbsd14)");` to the top of the `build.rs` = note: see <https://doc.rust-lang.org/nightly/rustc/check-cfg/cargo-specifics.html> for more information about checking conditional configuration warning: unexpected `cfg` condition name: `fbsd14` --> /wrkdirs/usr/ports/biology/coverm/work/CoverM-0.7.0/cargo-crates/nix-0.26.4/src/sys/aio.rs:863:16 | 863 | #[cfg_attr(not(fbsd14), doc = " ```no_run")] | ^^^^^^ | = help: consider using a Cargo feature instead = help: or consider adding in `Cargo.toml` the `check-cfg` lint config for the lint: [lints.rust] unexpected_cfgs = { level = "warn", check-cfg = ['cfg(fbsd14)'] } = help: or consider adding `println!("cargo::rustc-check-cfg=cfg(fbsd14)");` to the top of the `build.rs` = note: see <https://doc.rust-lang.org/nightly/rustc/check-cfg/cargo-specifics.html> for more information about checking conditional configuration [hts-sys 2.1.4] exit status: 0 [hts-sys 2.1.4] exit status: 0 [hts-sys 2.1.4] exit status: 0 [hts-sys 2.1.4] exit status: 0 [hts-sys 2.1.4] exit status: 0 [hts-sys 2.1.4] exit status: 0 [hts-sys 2.1.4] exit status: 0 [hts-sys 2.1.4] exit status: 0 [hts-sys 2.1.4] exit status: 0 [hts-sys 2.1.4] exit status: 0 [hts-sys 2.1.4] exit status: 0 [hts-sys 2.1.4] exit status: 0 [hts-sys 2.1.4] cargo:rerun-if-env-changed=AR_aarch64-unknown-freebsd [hts-sys 2.1.4] AR_aarch64-unknown-freebsd = None [hts-sys 2.1.4] cargo:rerun-if-env-changed=AR_aarch64_unknown_freebsd [hts-sys 2.1.4] AR_aarch64_unknown_freebsd = None [hts-sys 2.1.4] cargo:rerun-if-env-changed=HOST_AR [hts-sys 2.1.4] HOST_AR = None [hts-sys 2.1.4] cargo:rerun-if-env-changed=AR [hts-sys 2.1.4] AR = None [hts-sys 2.1.4] cargo:rerun-if-env-changed=ARFLAGS_aarch64-unknown-freebsd [hts-sys 2.1.4] ARFLAGS_aarch64-unknown-freebsd = None [hts-sys 2.1.4] cargo:rerun-if-env-changed=ARFLAGS_aarch64_unknown_freebsd [hts-sys 2.1.4] ARFLAGS_aarch64_unknown_freebsd = None [hts-sys 2.1.4] cargo:rerun-if-env-changed=HOST_ARFLAGS [hts-sys 2.1.4] HOST_ARFLAGS = None [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-4b4ad379bf8dca46/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-4b4ad379bf8dca46/out [hts-sys 2.1.4] cargo:include=/wrkdirs/usr/ports/biology/coverm/work/target/release/build/hts-sys-4b4ad379bf8dca46/out/include [hts-sys 2.1.4] cargo:libdir=/wrkdirs/usr/ports/biology/coverm/work/target/release/build/hts-sys-4b4ad379bf8dca46/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_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-4b4ad379bf8dca46/out /usr/local/bin/rustc --crate-name hts_sys --edition=2018 /wrkdirs/usr/ports/biology/coverm/work/CoverM-0.7.0/cargo-crates/h ts-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=9c31d8f88e8e2914 -C extra-filename=-9c31d8f88e8e2914 --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-ccae13e4e043aaab.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-4b4ad379bf8dca46/out -l static=hts -L native=/wrkdirs/usr/ports/biology/ coverm/work/target/release/build/libz-sys-082060cb9d62b814/out/lib -L native=/wrkdirs/usr/ports/biology/coverm/work/target/release/build/libz-sys-082060cb9d62b814/out/lib64` warning: fields `1` and `2` are never read --> /wrkdirs/usr/ports/biology/coverm/work/CoverM-0.7.0/cargo-crates/nix-0.26.4/src/sys/sendfile.rs:76:13 | 74 | struct SendfileHeaderTrailer<'a>( | --------------------- fields in this struct 75 | libc::sf_hdtr, 76 | Option<Vec<IoSlice<'a>>>, | ^^^^^^^^^^^^^^^^^^^^^^^^ 77 | Option<Vec<IoSlice<'a>>>, | ^^^^^^^^^^^^^^^^^^^^^^^^ | = help: consider removing these fields = note: `SendfileHeaderTrailer` has derived impls for the traits `Debug` and `Clone`, but these are intentionally ignored during dead code analysis note: the lint level is defined here --> /wrkdirs/usr/ports/biology/coverm/work/CoverM-0.7.0/cargo-crates/nix-0.26.4/src/lib.rs:48:9 | 48 | #![deny(unused)] | ^^^^^^ = note: `#[warn(dead_code)]` implied by `#[warn(unused)]` 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_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 --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=b830581374d33150 -C extra-filename=-b830581374d33150 --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-192992197a339a01.rmeta --extern byteorder=/wrkdirs/usr/ports/biology/coverm/work/target/release/deps/libbyteorder-2cadf277e1149948.rmeta --extern custom_derive=/wrkdirs/usr/ports/biology/coverm/work/target/release/deps/libcustom_derive-d9759bfbc305359d.rmeta --extern derive_ne w=/wrkdirs/usr/ports/biology/coverm/work/target/release/deps/libderive_new-68ba6804c1ede7db.so --extern hts_sys=/wrkdirs/usr/ports/biology/coverm/work/target/release/deps/libhts_sys-9c31d8f88e8e2914.rmeta --extern ieee754=/wrkdirs/usr/ports/biology/coverm/work/target/release/deps/libieee754-40958a4ad43649b4.rmeta --extern lazy_static=/wrkdirs/usr/ports/biology/coverm/work/target/release/deps/liblazy_static-a46b912a5f7c3eb3.rmeta --extern libc=/wrkdirs/usr/ports/biology/coverm/work/target/release/deps/liblibc-b8a665b29b8f01aa.rmeta --extern linear_map=/wrkdirs/usr/ports/biology/coverm/work/target/release/deps/liblinear_map-8cb00a557bd2f102.rmeta --extern newtype_derive=/wrkdirs/usr/ports/biology/coverm/work/target/release/deps/libnewtype_derive-5f764ab46381fdea.rmeta --extern regex=/wrkdirs/usr/ports/biology/coverm/work/target/release/deps/libregex-2c90b3c3726e333b.rmeta --extern thiserror=/wrkdirs/usr/ports/biology/coverm/work/target/release/deps/libthiserror-c2c283808a37a4e 9.rmeta --extern url=/wrkdirs/usr/ports/biology/coverm/work/target/release/deps/liburl-b6d1c45bd2009e27.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-4b4ad379bf8dca46/out -L native=/wrkdirs/usr/ports/biology/coverm/work/target/release/build/libz-sys-082060cb9d62b814/out/lib -L native=/wrkdirs/usr/ports/biology/coverm/work/target/release/build/libz-sys-082060cb9d62b814/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:2324:17 | 2319 | let ret = hts_sys::bam_mods_query_type( | ---------------------------- arguments to this function are incorrect ... 2324 | &mut canonical, | ^^^^^^^^^^^^^^ expected `*mut u8`, found `&mut i8` | = note: expected raw pointer `*mut u8` found mutable reference `&mut i8` note: function defined here --> /wrkdirs/usr/ports/biology/coverm/work/target/release/build/hts-sys-4b4ad379bf8dca46/out/bindings.rs:9439:12 | 9439 | pub fn bam_mods_query_type( | ^^^^^^^^^^^^^^^^^^^ For more information about this error, try `rustc --explain E0308`. error: could not compile `rust-htslib` (lib) due to 1 previous error 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_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 --crate-name rust_htslib --edition=2018 /wrkdirs/usr/ports/biology/coverm/work/CoverM-0.7.0/carg o-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=b830581374d33150 -C extra-filename=-b830581374d33150 --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-192992197a339a01.rmeta --extern byteorder=/wrkdirs/usr/ports/biology/coverm/work/target/release/deps/libbyteorder-2cadf277e1149948.rmeta --extern custom_derive=/wrkdirs/usr/ports/biology/coverm/work/target/release/deps/libcustom_derive-d9759bfbc305359d.r meta --extern derive_new=/wrkdirs/usr/ports/biology/coverm/work/target/release/deps/libderive_new-68ba6804c1ede7db.so --extern hts_sys=/wrkdirs/usr/ports/biology/coverm/work/target/release/deps/libhts_sys-9c31d8f88e8e2914.rmeta --extern ieee754=/wrkdirs/usr/ports/biology/coverm/work/target/release/deps/libieee754-40958a4ad43649b4.rmeta --extern lazy_static=/wrkdirs/usr/ports/biology/coverm/work/target/release/deps/liblazy_static-a46b912a5f7c3eb3.rmeta --extern libc=/wrkdirs/usr/ports/biology/coverm/work/target/release/deps/liblibc-b8a665b29b8f01aa.rmeta --extern linear_map=/wrkdirs/usr/ports/biology/coverm/work/target/release/deps/liblinear_map-8cb00a557bd2f102.rmeta --extern newtype_derive=/wrkdirs/usr/ports/biology/coverm/work/target/release/deps/libnewtype_derive-5f764ab46381fdea.rmeta --extern regex=/wrkdirs/usr/ports/biology/coverm/work/target/release/deps/libregex-2c90b3c3726e333b.rmeta --extern thiserror=/wrkdirs/usr/ports/biology/coverm/work/target/release/deps/libth iserror-c2c283808a37a4e9.rmeta --extern url=/wrkdirs/usr/ports/biology/coverm/work/target/release/deps/liburl-b6d1c45bd2009e27.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-4b4ad379bf8dca46/out -L native=/wrkdirs/usr/ports/biology/coverm/work/target/release/build/libz-sys-082060cb9d62b814/out/lib -L native=/wrkdirs/usr/ports/biology/coverm/work/target/release/build/libz-sys-082060cb9d62b814/out/lib64` (exit status: 1) warning: build failed, waiting for other jobs to finish... warning: `nix` (lib) generated 9 warnings *** Error code 101 Stop. make: stopped in /usr/ports/biology/coverm
