[package - 141arm64-default][biology/coverm] Failed for coverm-0.7.0 in build
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Date: Wed, 06 Nov 2024 19:45:39 UTC
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/332c73b035e3/logs/coverm-0.7.0.log
Build URL: https://pkg-status.freebsd.org/ampere3/build.html?mastername=141arm64-default&build=332c73b035e3
Log:
=>> Building biology/coverm
build started at Wed Nov 6 19:39:42 UTC 2024
port directory: /usr/ports/biology/coverm
package name: coverm-0.7.0
building for: FreeBSD 141arm64-default-job-02 14.1-RELEASE-p5 FreeBSD 14.1-RELEASE-p5 arm64
maintained by: yuri@FreeBSD.org
Makefile datestamp: -rw-r--r-- 1 root wheel 5708 Oct 13 01:01 /usr/ports/biology/coverm/Makefile
Ports top last git commit: 332c73b035e
Ports top unclean checkout: no
Port dir last git commit: 293343cc113
Port dir unclean checkout: no
Poudriere version: poudriere-git-3.4.2
Host OSVERSION: 1500023
Jail OSVERSION: 1401000
Job Id: 02
---Begin Environment---
SHELL=/bin/sh
OSVERSION=1401000
UNAME_v=FreeBSD 14.1-RELEASE-p5
UNAME_r=14.1-RELEASE-p5
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/02/.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--
=======================<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
[141arm64-default-job-02] Installing pkg-1.21.3...
[141arm64-default-job-02] 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: 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
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)]`
[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.schroeder@tu-dortmund.de>:Johannes Köster <johannes.koester@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`
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.schroeder@tu-dortmund.de>:Johannes Köster <johannes.koester@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(
| ^^^^^^^^^^^^^^^^^^^
warning: `nix` (lib) generated 9 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_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 --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,l
ink -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_names' '--warn=clippy::needless_for_each' '--warn=clippy::needless_continue' '--warn=clippy::mutex_integer' '--allow=cli
ppy::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_methods' '--warn=clippy::expl_impl_clone_on_copy' '--warn=clippy::enum_glob_use' '--warn=clippy::empty_enum' '--warn=cli
ppy::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=45d6c09fbf4291bf -C extra-filename=-45d6c09fbf4291bf --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-008c328d2fba1639.rmeta --cap-lints warn -C target-cpu= -C link-arg=-fstack-protector-strong`
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.schroeder@tu-dortmund.de>:Johannes Köster <johannes.koester@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...
*** Error code 101
Stop.
make: stopped in /usr/ports/biology/coverm