From nobody Thu Nov 21 07:37:48 2024 X-Original-To: pkg-fallout@mlmmj.nyi.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2610:1c1:1:606c::19:1]) by mlmmj.nyi.freebsd.org (Postfix) with ESMTP id 4Xv97J36SXz5fNFl for ; Thu, 21 Nov 2024 07:37:48 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: from mxrelay.nyi.freebsd.org (mxrelay.nyi.freebsd.org [IPv6:2610:1c1:1:606c::19:3]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (4096 bits) server-digest SHA256 client-signature RSA-PSS (4096 bits) client-digest SHA256) (Client CN "mxrelay.nyi.freebsd.org", Issuer "R10" (verified OK)) by mx1.freebsd.org (Postfix) with ESMTPS id 4Xv97J1Rfhz51H6 for ; Thu, 21 Nov 2024 07:37:48 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1732174668; h=from:from:reply-to:subject:subject:date:date:message-id:message-id: to:to:cc:cc; bh=p+X+RU7GNwxHVFuEkJHQYKHlBBBSc1vwVj21igCkTT0=; b=c3xdMyf9JzVr0ThHhrMn39PfanVvd347IRAcsTcoze+urms1pPVRfBap+EGvbEQp8WUQ/j eo/OLXpuqzhmaROSj+4/yg+RyMdYkgpPr5Dq20+hppq1U8zWSjzAWbYHo05ev9p4oQkPDE 3at256kEkeXn/Coqijgc03QhD/cz6Y6X4xtY5x8xIzTVgPyXcCiZ/aIeDODD1WvGR5FSCm nfgHm3FezU+raJW/yRFnZP/IW5sbwdRDjqgURpH+NE2V/u9SL2R4N2VBXGitesb1Gglpyr LHit4DH9n0c930A0O/Uxx3+oUrI8dcavsPjpL56uOVP6HquL+Jan3psw0gSxig== ARC-Authentication-Results: i=1; mx1.freebsd.org; none ARC-Seal: i=1; s=dkim; d=freebsd.org; t=1732174668; a=rsa-sha256; cv=none; b=LPZyp8qgoTAmY3IfjqkclAFkH5JNUK7p0lDVBoSv5IgOwaGQs+Od2b+sE1NXGj7hxlyvQE +5tcY0PrgLe3mUmT9Fo+8YVQCt52aHY4xiA/o0za8IzdlGyeZENxDtA+Vg13AisBAoyIWa qN4fFGAWbN3k++L+GlK0nF+9mS5eF5BGlD3rVAw4d82UdwPfCXVAl5pqrbsp+SGFWHHRoY srKHG/MzU6KFJ+a88/5S+0wf1MEvMNKAHMgMgG3Z5hotEjVgkDd6dmBGUYFd6NAQ3niZ1c a793cszfEGQxxDsIdhAtO1TpsbuQHDJ+QEN6qQKMP/Z6gLDjKAsX9gmKWHiJAQ== Received: from ampere3.nyi.freebsd.org (ampere3.nyi.freebsd.org [IPv6:2610:1c1:1:6080::16:26]) by mxrelay.nyi.freebsd.org (Postfix) with ESMTP id 4Xv97J0qvgzTHn for ; Thu, 21 Nov 2024 07:37:48 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: from root (uid 0) (envelope-from pkg-fallout@FreeBSD.org) id 62e4 by ampere3.nyi.freebsd.org (DragonFly Mail Agent v0.13+ on ampere3.nyi.freebsd.org); Thu, 21 Nov 2024 07:37:48 +0000 To: yuri@FreeBSD.org Subject: [package - 141arm64-default][biology/coverm] Failed for coverm-0.7.0_1 in build Cc: pkg-fallout@FreeBSD.org Date: Thu, 21 Nov 2024 07:37:48 +0000 Message-Id: <673ee34c.62e4.1878dc0d@ampere3.nyi.freebsd.org> From: List-Id: Fallout logs from package building List-Archive: https://lists.freebsd.org/archives/freebsd-pkg-fallout List-Help: List-Post: List-Subscribe: List-Unsubscribe: Sender: owner-freebsd-pkg-fallout@FreeBSD.org You are receiving this mail as a port that you maintain is failing to build on the FreeBSD package build server. Please investigate the failure and submit a PR to fix build. Maintainer: yuri@FreeBSD.org Log URL: https://pkg-status.freebsd.org/ampere3/data/141arm64-default/203aa1081a24/logs/coverm-0.7.0_1.log Build URL: https://pkg-status.freebsd.org/ampere3/build.html?mastername=141arm64-default&build=203aa1081a24 Log: =>> Building biology/coverm build started at Thu Nov 21 07:30:37 UTC 2024 port directory: /usr/ports/biology/coverm package name: coverm-0.7.0_1 building for: FreeBSD 141arm64-default-job-03 14.1-RELEASE-p6 FreeBSD 14.1-RELEASE-p6 arm64 maintained by: yuri@FreeBSD.org Makefile datestamp: -rw-r--r-- 1 root wheel 5724 Nov 9 01:01 /usr/ports/biology/coverm/Makefile Ports top last git commit: 203aa1081a2 Ports top unclean checkout: no Port dir last git commit: ca048c2884d Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.2 Host OSVERSION: 1500023 Jail OSVERSION: 1401000 Job Id: 03 ---Begin Environment--- SHELL=/bin/sh OSVERSION=1401000 UNAME_v=FreeBSD 14.1-RELEASE-p6 UNAME_r=14.1-RELEASE-p6 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/141arm64-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/141arm64-default/03/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS MASTERNAME=141arm64-default SCRIPTPREFIX=/usr/local/share/poudriere SCRIPTNAME=bulk.sh OLDPWD=/usr/local/poudriere/data/.m/141arm64-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-- yuri@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=14.1 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-- =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> License AGPLv3 accepted by the user =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> coverm-0.7.0_1 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.21.3.pkg [141arm64-default-job-03] Installing pkg-1.21.3... [141arm64-default-job-03] Extracting pkg-1.21.3: .......... done ===> coverm-0.7.0_1 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of coverm-0.7.0_1 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== 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_1 for building =========================================================================== =================================================== ===== 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_1 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. = help: or consider adding `println!("cargo::rustc-check-cfg=cfg(fbsd14)");` to the top of the `build.rs` = note: see 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/fcntl.rs:785:16 | 785 | #[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 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 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 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 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 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] 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-15b6249c1fdc8a27/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-15b6249c1fdc8a27/out [hts-sys 2.1.4] cargo:include=/wrkdirs/usr/ports/biology/coverm/work/target/release/build/hts-sys-15b6249c1fdc8a27/out/include [hts-sys 2.1.4] cargo:libdir=/wrkdirs/usr/ports/biology/coverm/work/target/release/build/hts-sys-15b6249c1fdc8a27/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 :Johannes Köster ' 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-15b6249c1fdc8a27/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=65d618490234ed78 -C extra-filename=-65d618490234ed78 --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-cdc2d126542b5140.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-15b6249c1fdc8a27/out -l static=hts -L native=/wrkdirs/usr/ports/biology/ coverm/work/target/release/build/libz-sys-cfc6856b2a9892f9/out/lib -L native=/wrkdirs/usr/ports/biology/coverm/work/target/release/build/libz-sys-cfc6856b2a9892f9/out/lib64` 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 :Johannes Köster ' 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=05e880bf9263409a -C extra-filename=-05e880bf9263409a --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-ca1606d4b60108a0.rmeta --extern byteorder=/wrkdirs/usr/ports/biology/coverm/work/target/release/deps/libbyteorder-34566ed80ec22e44.rmeta --extern custom_derive=/wrkdirs/usr/ports/biology/coverm/work/target/release/deps/libcustom_derive-cb73ac6bc0a04f63.rmeta --extern derive_ne w=/wrkdirs/usr/ports/biology/coverm/work/target/release/deps/libderive_new-cbb2cc305e5577dd.so --extern hts_sys=/wrkdirs/usr/ports/biology/coverm/work/target/release/deps/libhts_sys-65d618490234ed78.rmeta --extern ieee754=/wrkdirs/usr/ports/biology/coverm/work/target/release/deps/libieee754-473ff2d028ca13bf.rmeta --extern lazy_static=/wrkdirs/usr/ports/biology/coverm/work/target/release/deps/liblazy_static-73d579eceeaabdb5.rmeta --extern libc=/wrkdirs/usr/ports/biology/coverm/work/target/release/deps/liblibc-01cf28ac3966abb3.rmeta --extern linear_map=/wrkdirs/usr/ports/biology/coverm/work/target/release/deps/liblinear_map-fb2e81e18d35e095.rmeta --extern newtype_derive=/wrkdirs/usr/ports/biology/coverm/work/target/release/deps/libnewtype_derive-d142a46eb229b627.rmeta --extern regex=/wrkdirs/usr/ports/biology/coverm/work/target/release/deps/libregex-8c146cfa28554078.rmeta --extern thiserror=/wrkdirs/usr/ports/biology/coverm/work/target/release/deps/libthiserror-eef5fc599dddbd8 4.rmeta --extern url=/wrkdirs/usr/ports/biology/coverm/work/target/release/deps/liburl-045cb10cbd4f35d5.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-15b6249c1fdc8a27/out -L native=/wrkdirs/usr/ports/biology/coverm/work/target/release/build/libz-sys-cfc6856b2a9892f9/out/lib -L native=/wrkdirs/usr/ports/biology/coverm/work/target/release/build/libz-sys-cfc6856b2a9892f9/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-15b6249c1fdc8a27/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 :Johannes Köster ' 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=05e880bf9263409a -C extra-filename=-05e880bf9263409a --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-ca1606d4b60108a0.rmeta --extern byteorder=/wrkdirs/usr/ports/biology/coverm/work/target/release/deps/libbyteorder-34566ed80ec22e44.rmeta --extern custom_derive=/wrkdirs/usr/ports/biology/coverm/work/target/release/deps/libcustom_derive-cb73ac6bc0a04f63.r meta --extern derive_new=/wrkdirs/usr/ports/biology/coverm/work/target/release/deps/libderive_new-cbb2cc305e5577dd.so --extern hts_sys=/wrkdirs/usr/ports/biology/coverm/work/target/release/deps/libhts_sys-65d618490234ed78.rmeta --extern ieee754=/wrkdirs/usr/ports/biology/coverm/work/target/release/deps/libieee754-473ff2d028ca13bf.rmeta --extern lazy_static=/wrkdirs/usr/ports/biology/coverm/work/target/release/deps/liblazy_static-73d579eceeaabdb5.rmeta --extern libc=/wrkdirs/usr/ports/biology/coverm/work/target/release/deps/liblibc-01cf28ac3966abb3.rmeta --extern linear_map=/wrkdirs/usr/ports/biology/coverm/work/target/release/deps/liblinear_map-fb2e81e18d35e095.rmeta --extern newtype_derive=/wrkdirs/usr/ports/biology/coverm/work/target/release/deps/libnewtype_derive-d142a46eb229b627.rmeta --extern regex=/wrkdirs/usr/ports/biology/coverm/work/target/release/deps/libregex-8c146cfa28554078.rmeta --extern thiserror=/wrkdirs/usr/ports/biology/coverm/work/target/release/deps/libth iserror-eef5fc599dddbd84.rmeta --extern url=/wrkdirs/usr/ports/biology/coverm/work/target/release/deps/liburl-045cb10cbd4f35d5.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-15b6249c1fdc8a27/out -L native=/wrkdirs/usr/ports/biology/coverm/work/target/release/build/libz-sys-cfc6856b2a9892f9/out/lib -L native=/wrkdirs/usr/ports/biology/coverm/work/target/release/build/libz-sys-cfc6856b2a9892f9/out/lib64` (exit status: 1) warning: build failed, waiting for other jobs to finish... 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>>, | ^^^^^^^^^^^^^^^^^^^^^^^^ 77 | Option>>, | ^^^^^^^^^^^^^^^^^^^^^^^^ | = 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)]` warning: `nix` (lib) generated 9 warnings *** Error code 101 Stop. make: stopped in /usr/ports/biology/coverm