[package - 135releng-armv7-default][biology/coverm] Failed for coverm-0.7.0_7 in build
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Date: Fri, 18 Jul 2025 20:30:37 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/135releng-armv7-default/b3423aefe7f1/logs/coverm-0.7.0_7.log
Build URL: https://pkg-status.freebsd.org/ampere3/build.html?mastername=135releng-armv7-default&build=b3423aefe7f1
Log:
=>> Building biology/coverm
build started at Fri Jul 18 20:23:07 UTC 2025
port directory: /usr/ports/biology/coverm
package name: coverm-0.7.0_7
building for: FreeBSD 135releng-armv7-default-job-11 13.5-RELEASE-p2 FreeBSD 13.5-RELEASE-p2 1305000 arm
maintained by: yuri@FreeBSD.org
Makefile datestamp: -rw-r--r-- 1 root wheel 5806 Jul 8 01:02 /usr/ports/biology/coverm/Makefile
Ports top last git commit: b3423aefe7f
Ports top unclean checkout: no
Port dir last git commit: f3f7e555b06
Port dir unclean checkout: no
Poudriere version: poudriere-git-3.4.2-12-g74a54a88
Host OSVERSION: 1500035
Jail OSVERSION: 1305000
Job Id: 11
---Begin Environment---
SHELL=/bin/csh
OSVERSION=1305000
UNAME_v=FreeBSD 13.5-RELEASE-p2 1305000
UNAME_r=13.5-RELEASE-p2
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=3.4.2-12-g74a54a88
MASTERMNT=/usr/local/poudriere/data/.m/135releng-armv7-default/ref
LC_COLLATE=C
POUDRIERE_BUILD_TYPE=bulk
PACKAGE_BUILDING=yes
SAVED_TERM=
OUTPUT_REDIRECTED_STDERR=4
OUTPUT_REDIRECTED=1
PWD=/usr/local/poudriere/data/.m/135releng-armv7-default/11/.p
OUTPUT_REDIRECTED_STDOUT=3
P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS
MASTERNAME=135releng-armv7-default
SCRIPTPREFIX=/usr/local/share/poudriere
SCRIPTNAME=bulk.sh
OLDPWD=/usr/local/poudriere/data/.m/135releng-armv7-default/ref/.p/pool
POUDRIERE_PKGNAME=poudriere-git-3.4.2-12-g74a54a88
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=" " 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_INSTALL_DATA="install -m 0644
" BSD_INSTALL_MAN="install -m 444"
--End MAKE_ENV--
--PLIST_SUB--
OSREL=13.5 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/coverm" EXAMPLESDIR="share/examples/coverm" DATADIR="share/coverm" WWWDIR="www/coverm" ETCDIR="etc/coverm"
--End PLIST_SUB--
--SUB_LIST--
PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/coverm DOCSDIR=/usr/local/share/doc/coverm EXAMPLESDIR=/usr/local/share/examples/coverm WWWDIR=/usr/local/www/coverm ETCDIR=/usr/local/etc/coverm
--End SUB_LIST--
---Begin make.conf---
# XXX: We really need this but cannot use it while 'make checksum' does not
# try the next mirror on checksum failure. It currently retries the same
# failed mirror and then fails rather then trying another. It *does*
# try the next if the size is mismatched though.
#MASTER_SITE_FREEBSD=yes
# Build ALLOW_MAKE_JOBS_PACKAGES with 3 jobs
MAKE_JOBS_NUMBER=3
USE_PACKAGE_DEPENDS=yes
BATCH=yes
WRKDIRPREFIX=/wrkdirs
PORTSDIR=/usr/ports
PACKAGES=/packages
DISTDIR=/distfiles
PACKAGE_BUILDING=yes
PACKAGE_BUILDING_FLAVORS=yes
#### ####
# XXX: We really need this but cannot use it while 'make checksum' does not
# try the next mirror on checksum failure. It currently retries the same
# failed mirror and then fails rather then trying another. It *does*
# try the next if the size is mismatched though.
#MASTER_SITE_FREEBSD=yes
# Build ALLOW_MAKE_JOBS_PACKAGES with 3 jobs
MAKE_JOBS_NUMBER=3
#### Misc Poudriere ####
.include "/etc/make.conf.ports_env"
GID=0
UID=0
---End make.conf---
--Resource limits--
cpu time (seconds, -t) unlimited
file size (512-blocks, -f) unlimited
data seg size (kbytes, -d) 524288
stack size (kbytes, -s) 65536
core file size (512-blocks, -c) unlimited
max memory size (kbytes, -m) unlimited
locked memory (kbytes, -l) unlimited
max user processes (-u) 89999
open files (-n) 8192
virtual mem size (kbytes, -v) unlimited
swap limit (kbytes, -w) unlimited
socket buffer size (bytes, -b) unlimited
pseudo-terminals (-p) unlimited
kqueues (-k) unlimited
umtx shared locks (-o) unlimited
--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_7 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-2.2.1.pkg
[135releng-armv7-default-job-11] Installing pkg-2.2.1...
[135releng-armv7-default-job-11] Extracting pkg-2.2.1: .......... done
===> coverm-0.7.0_7 depends on file: /usr/local/sbin/pkg - found
===> Returning to build of coverm-0.7.0_7
===========================================================================
=======================<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_7 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_7 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.
<snip>
--> /wrkdirs/usr/ports/biology/coverm/work/CoverM-0.7.0/cargo-crates/rand-0.4.6/src/lib.rs:411:36
|
411 | let result: f64 = unsafe { mem::transmute(tmp) };
| ^^^^^^^^^^^^^^^^^^^ help: replace this with: `f64::from_bits(tmp)`
warning: `disjoint` (lib) generated 6 warnings
Compiling remove_dir_all v0.5.3
Running `CARGO=/usr/local/bin/cargo CARGO_CRATE_NAME=remove_dir_all CARGO_MANIFEST_DIR=/wrkdirs/usr/ports/biology/coverm/work/CoverM-0.7.0/cargo-crates/remove_dir_all-0.5.3 CARGO_MANIFEST_PATH=/wrkdirs/usr/ports/biology/coverm/work/CoverM-0.7.0/cargo-crates/remove_dir_all-0.5.3/Cargo.toml CARGO_PKG_AUTHORS='Aaronepower <theaaronepower@gmail.com>' CARGO_PKG_DESCRIPTION='A safe, reliable implementation of remove_dir_all for Windows' CARGO_PKG_HOMEPAGE='' CARGO_PKG_LICENSE=MIT/Apache-2.0 CARGO_PKG_LICENSE_FILE='' CARGO_PKG_NAME=remove_dir_all CARGO_PKG_README=README.md CARGO_PKG_REPOSITORY='https://github.com/XAMPPRocky/remove_dir_all.git' CARGO_PKG_RUST_VERSION='' CARGO_PKG_VERSION=0.5.3 CARGO_PKG_VERSION_MAJOR=0 CARGO_PKG_VERSION_MINOR=5 CARGO_PKG_VERSION_PATCH=3 CARGO_PKG_VERSION_PRE='' LD_LIBRARY_PATH=/wrkdirs/usr/ports/biology/coverm/work/target/release/deps /usr/local/bin/rustc --crate-name remove_dir_all --edition=2015 /wrkdirs/usr/ports/biology/coverm/work/CoverM-0
.7.0/cargo-crates/remove_dir_all-0.5.3/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,test)' --check-cfg 'cfg(feature, values())' -C metadata=2a887be86f6b2e30 -C extra-filename=-662a9fe23621d874 --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 --cap-lints warn -C target-cpu=`
Compiling linear-map v1.2.0
Running `CARGO=/usr/local/bin/cargo CARGO_CRATE_NAME=linear_map CARGO_MANIFEST_DIR=/wrkdirs/usr/ports/biology/coverm/work/CoverM-0.7.0/cargo-crates/linear-map-1.2.0 CARGO_MANIFEST_PATH=/wrkdirs/usr/ports/biology/coverm/work/CoverM-0.7.0/cargo-crates/linear-map-1.2.0/Cargo.toml CARGO_PKG_AUTHORS='Andrew Paseltiner <apaseltiner@gmail.com>:Tobias Bucher <tobiasbucher5991@gmail.com>' CARGO_PKG_DESCRIPTION='A map implemented by searching linearly in a vector.' CARGO_PKG_HOMEPAGE='' CARGO_PKG_LICENSE=MIT/Apache-2.0 CARGO_PKG_LICENSE_FILE='' CARGO_PKG_NAME=linear-map CARGO_PKG_README=README.md CARGO_PKG_REPOSITORY='https://github.com/contain-rs/linear-map' CARGO_PKG_RUST_VERSION='' CARGO_PKG_VERSION=1.2.0 CARGO_PKG_VERSION_MAJOR=1 CARGO_PKG_VERSION_MINOR=2 CARGO_PKG_VERSION_PATCH=0 CARGO_PKG_VERSION_PRE='' LD_LIBRARY_PATH=/wrkdirs/usr/ports/biology/coverm/work/target/release/deps /usr/local/bin/rustc --crate-name linear_map --edition=2015 /wrkdirs/usr/ports/biology/coverm/work
/CoverM-0.7.0/cargo-crates/linear-map-1.2.0/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,test)' --check-cfg 'cfg(feature, values("nightly", "serde", "serde_impl", "serde_test"))' -C metadata=efa03833427e4c36 -C extra-filename=-2095da7606a15fa5 --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 --cap-lints warn -C target-cpu=`
warning: `rand` (lib) generated 16 warnings
Compiling ieee754 v0.2.6
Running `CARGO=/usr/local/bin/cargo CARGO_CRATE_NAME=ieee754 CARGO_MANIFEST_DIR=/wrkdirs/usr/ports/biology/coverm/work/CoverM-0.7.0/cargo-crates/ieee754-0.2.6 CARGO_MANIFEST_PATH=/wrkdirs/usr/ports/biology/coverm/work/CoverM-0.7.0/cargo-crates/ieee754-0.2.6/Cargo.toml CARGO_PKG_AUTHORS='Huon Wilson <dbau.pp@gmail.com>' CARGO_PKG_DESCRIPTION='Low-level manipulations of IEEE754 floating-point numbers.
' CARGO_PKG_HOMEPAGE='https://github.com/huonw/ieee754' CARGO_PKG_LICENSE=MIT/Apache-2.0 CARGO_PKG_LICENSE_FILE='' CARGO_PKG_NAME=ieee754 CARGO_PKG_README=README.md CARGO_PKG_REPOSITORY='https://github.com/huonw/ieee754' CARGO_PKG_RUST_VERSION='' CARGO_PKG_VERSION=0.2.6 CARGO_PKG_VERSION_MAJOR=0 CARGO_PKG_VERSION_MINOR=2 CARGO_PKG_VERSION_PATCH=6 CARGO_PKG_VERSION_PRE='' LD_LIBRARY_PATH=/wrkdirs/usr/ports/biology/coverm/work/target/release/deps /usr/local/bin/rustc --crate-name ieee754 --edition=2015 /wrkdirs/usr/ports/biology/coverm/work/CoverM-0.7.0/cargo-crates/ieee754-0.2.6/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,test)' --check-cfg 'cfg(feature, values("unstable"))' -C metadata=fdb7ed0eda862cc9 -C extra-filename=-37ec808844007e98 --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 --cap-lints warn -C target-cpu=`
warning: unnecessary transmute
--> /wrkdirs/usr/ports/biology/coverm/work/CoverM-0.7.0/cargo-crates/ieee754-0.2.6/src/impls.rs:93:25
|
93 | unsafe {mem::transmute(self)}
| ^^^^^^^^^^^^^^^^^^^^ help: replace this with: `f32::to_bits(self)`
...
517 | mk_impl!(f32, u32, i32, i16, u8, u32, 8, 23);
| -------------------------------------------- in this macro invocation
|
= note: `#[warn(unnecessary_transmutes)]` on by default
= note: this warning originates in the macro `mk_impl` (in Nightly builds, run with -Z macro-backtrace for more info)
warning: unnecessary transmute
--> /wrkdirs/usr/ports/biology/coverm/work/CoverM-0.7.0/cargo-crates/ieee754-0.2.6/src/impls.rs:97:25
|
97 | unsafe {mem::transmute(bits)}
| ^^^^^^^^^^^^^^^^^^^^ help: replace this with: `f32::from_bits(bits)`
...
517 | mk_impl!(f32, u32, i32, i16, u8, u32, 8, 23);
| -------------------------------------------- in this macro invocation
|
= note: this warning originates in the macro `mk_impl` (in Nightly builds, run with -Z macro-backtrace for more info)
warning: unnecessary transmute
--> /wrkdirs/usr/ports/biology/coverm/work/CoverM-0.7.0/cargo-crates/ieee754-0.2.6/src/impls.rs:93:25
|
93 | unsafe {mem::transmute(self)}
| ^^^^^^^^^^^^^^^^^^^^ help: replace this with: `f64::to_bits(self)`
...
518 | mk_impl!(f64, u64, i64, i16, u16, u64, 11, 52);
| ---------------------------------------------- in this macro invocation
|
= note: this warning originates in the macro `mk_impl` (in Nightly builds, run with -Z macro-backtrace for more info)
warning: unnecessary transmute
--> /wrkdirs/usr/ports/biology/coverm/work/CoverM-0.7.0/cargo-crates/ieee754-0.2.6/src/impls.rs:97:25
|
97 | unsafe {mem::transmute(bits)}
| ^^^^^^^^^^^^^^^^^^^^ help: replace this with: `f64::from_bits(bits)`
...
518 | mk_impl!(f64, u64, i64, i16, u16, u64, 11, 52);
| ---------------------------------------------- in this macro invocation
|
= note: this warning originates in the macro `mk_impl` (in Nightly builds, run with -Z macro-backtrace for more info)
Compiling tempdir v0.3.7
Running `CARGO=/usr/local/bin/cargo CARGO_CRATE_NAME=tempdir CARGO_MANIFEST_DIR=/wrkdirs/usr/ports/biology/coverm/work/CoverM-0.7.0/cargo-crates/tempdir-0.3.7 CARGO_MANIFEST_PATH=/wrkdirs/usr/ports/biology/coverm/work/CoverM-0.7.0/cargo-crates/tempdir-0.3.7/Cargo.toml CARGO_PKG_AUTHORS='The Rust Project Developers' CARGO_PKG_DESCRIPTION='A library for managing a temporary directory and deleting all contents when it'\''s
dropped.
' CARGO_PKG_HOMEPAGE='https://github.com/rust-lang/tempdir' CARGO_PKG_LICENSE=MIT/Apache-2.0 CARGO_PKG_LICENSE_FILE='' CARGO_PKG_NAME=tempdir CARGO_PKG_README=README.md CARGO_PKG_REPOSITORY='https://github.com/rust-lang/tempdir' CARGO_PKG_RUST_VERSION='' CARGO_PKG_VERSION=0.3.7 CARGO_PKG_VERSION_MAJOR=0 CARGO_PKG_VERSION_MINOR=3 CARGO_PKG_VERSION_PATCH=7 CARGO_PKG_VERSION_PRE='' LD_LIBRARY_PATH=/wrkdirs/usr/ports/biology/coverm/work/target/release/deps /usr/local/bin/rustc --crate-name tempdir --edition=2015 /wrkdirs/usr/ports/biology/coverm/work/CoverM-0.7.0/cargo-crates/tempdir-0.3.7/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,test)' --check-cfg 'cfg(feature, values())' -C metadata=0c17d3ca5ecc2d7c -C extra-filename=-443cfe2dd55c0c78 --out-dir /wrkdirs/usr/ports/biology/coverm/work/target/r
elease/deps -C strip=symbols -L dependency=/wrkdirs/usr/ports/biology/coverm/work/target/release/deps --extern rand=/wrkdirs/usr/ports/biology/coverm/work/target/release/deps/librand-28950a50c837a92c.rmeta --extern remove_dir_all=/wrkdirs/usr/ports/biology/coverm/work/target/release/deps/libremove_dir_all-662a9fe23621d874.rmeta --cap-lints warn -C target-cpu=`
warning: `ieee754` (lib) generated 4 warnings
Compiling rust-htslib v0.44.1
Running `CARGO=/usr/local/bin/cargo CARGO_CRATE_NAME=rust_htslib CARGO_MANIFEST_DIR=/wrkdirs/usr/ports/biology/coverm/work/CoverM-0.7.0/cargo-crates/rust-htslib-0.44.1 CARGO_MANIFEST_PATH=/wrkdirs/usr/ports/biology/coverm/work/CoverM-0.7.0/cargo-crates/rust-htslib-0.44.1/Cargo.toml CARGO_PKG_AUTHORS='Christopher Schröder <christopher.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 --cr
ate-name rust_htslib --edition=2018 /wrkdirs/usr/ports/biology/coverm/work/CoverM-0.7.0/cargo-crates/rust-htslib-0.44.1/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C panic=abort -C linker-plugin-lto -C codegen-units=1 --check-cfg 'cfg(docsrs,test)' --check-cfg 'cfg(feature, values("bindgen", "bzip2", "curl", "default", "gcs", "libdeflate", "lzma", "s3", "serde", "serde_bytes", "serde_feature", "static"))' -C metadata=4f76b85ccc0f311d -C extra-filename=-c66c9e8616a92bc2 --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-43e822fa0dad2cfa.rmeta --extern byteorder=/wrkdirs/usr/ports/biology/coverm/work/target/release/deps/libbyteorder-b80956c97f283fcf.rmeta --extern custom_deri
ve=/wrkdirs/usr/ports/biology/coverm/work/target/release/deps/libcustom_derive-42ab22c6fd92b282.rmeta --extern derive_new=/wrkdirs/usr/ports/biology/coverm/work/target/release/deps/libderive_new-06696b8a7093e8c9.so --extern hts_sys=/wrkdirs/usr/ports/biology/coverm/work/target/release/deps/libhts_sys-c26ba8ec75b3dd26.rmeta --extern ieee754=/wrkdirs/usr/ports/biology/coverm/work/target/release/deps/libieee754-37ec808844007e98.rmeta --extern lazy_static=/wrkdirs/usr/ports/biology/coverm/work/target/release/deps/liblazy_static-94dbea200700be9c.rmeta --extern libc=/wrkdirs/usr/ports/biology/coverm/work/target/release/deps/liblibc-a6a7e02893365e9c.rmeta --extern linear_map=/wrkdirs/usr/ports/biology/coverm/work/target/release/deps/liblinear_map-2095da7606a15fa5.rmeta --extern newtype_derive=/wrkdirs/usr/ports/biology/coverm/work/target/release/deps/libnewtype_derive-d84c86f39cc705d8.rmeta --extern regex=/wrkdirs/usr/ports/biology/coverm/work/target/release/deps/libregex-d0de2b511
01d4bfd.rmeta --extern thiserror=/wrkdirs/usr/ports/biology/coverm/work/target/release/deps/libthiserror-ef7e45e6d240e6fa.rmeta --extern url=/wrkdirs/usr/ports/biology/coverm/work/target/release/deps/liburl-0cb3b73d39b7d724.rmeta --cap-lints warn -C target-cpu= -L native=/wrkdirs/usr/ports/biology/coverm/work/target/release/build/hts-sys-01897a4c42ff0bbf/out -L native=/wrkdirs/usr/ports/biology/coverm/work/target/release/build/libz-sys-8d49e24b54d2f48e/out/lib -L native=/wrkdirs/usr/ports/biology/coverm/work/target/release/build/libz-sys-8d49e24b54d2f48e/out/lib64`
Compiling galah v0.4.2
Running `CARGO=/usr/local/bin/cargo CARGO_CRATE_NAME=galah CARGO_MANIFEST_DIR=/wrkdirs/usr/ports/biology/coverm/work/CoverM-0.7.0/cargo-crates/galah-0.4.2 CARGO_MANIFEST_PATH=/wrkdirs/usr/ports/biology/coverm/work/CoverM-0.7.0/cargo-crates/galah-0.4.2/Cargo.toml CARGO_PKG_AUTHORS='Ben Woodcroft <benjwoodcroft@gmail.com>' CARGO_PKG_DESCRIPTION='Microbial genome dereplicator' CARGO_PKG_HOMEPAGE='https://github.com/wwood/galah' CARGO_PKG_LICENSE=GPL-3.0 CARGO_PKG_LICENSE_FILE='' CARGO_PKG_NAME=galah CARGO_PKG_README=README.md CARGO_PKG_REPOSITORY='https://github.com/wwood/galah' CARGO_PKG_RUST_VERSION='' CARGO_PKG_VERSION=0.4.2 CARGO_PKG_VERSION_MAJOR=0 CARGO_PKG_VERSION_MINOR=4 CARGO_PKG_VERSION_PATCH=2 CARGO_PKG_VERSION_PRE='' LD_LIBRARY_PATH=/wrkdirs/usr/ports/biology/coverm/work/target/release/deps /usr/local/bin/rustc --crate-name galah --edition=2018 /wrkdirs/usr/ports/biology/coverm/work/CoverM-0.7.0/cargo-crates/galah-0.4.2/src/lib.rs --error-format=json --json=dia
gnostic-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,test)' --check-cfg 'cfg(feature, values())' -C metadata=fed87bc8c9587600 -C extra-filename=-1c7139a3f95ba608 --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 ansi_term=/wrkdirs/usr/ports/biology/coverm/work/target/release/deps/libansi_term-750b257d2ac3ffbe.rmeta --extern bird_tool_utils=/wrkdirs/usr/ports/biology/coverm/work/target/release/deps/libbird_tool_utils-20c566922260520d.rmeta --extern bird_tool_utils_man=/wrkdirs/usr/ports/biology/coverm/work/target/release/deps/libbird_tool_utils_man-96003b767791ca03.rmeta --extern checkm=/wrkdirs/usr/ports/biology/coverm/work/target/release/deps/libcheckm-e4367c2d686bc85e.rmeta --extern clap=/wrkdirs/usr/ports/biology/coverm/wo
rk/target/release/deps/libclap-99e431e95235fbd2.rmeta --extern concurrent_queue=/wrkdirs/usr/ports/biology/coverm/work/target/release/deps/libconcurrent_queue-e860b51ba53630f8.rmeta --extern csv=/wrkdirs/usr/ports/biology/coverm/work/target/release/deps/libcsv-0f26dd9b4c277516.rmeta --extern disjoint=/wrkdirs/usr/ports/biology/coverm/work/target/release/deps/libdisjoint-ddcf6e25066ef8cf.rmeta --extern env_logger=/wrkdirs/usr/ports/biology/coverm/work/target/release/deps/libenv_logger-ed01e75b3897c09b.rmeta --extern finch=/wrkdirs/usr/ports/biology/coverm/work/target/release/deps/libfinch-5838fd2e0e4ceeb3.rlib --extern lazy_static=/wrkdirs/usr/ports/biology/coverm/work/target/release/deps/liblazy_static-94dbea200700be9c.rmeta --extern log=/wrkdirs/usr/ports/biology/coverm/work/target/release/deps/liblog-36ddd2d5107cf5ce.rmeta --extern needletail=/wrkdirs/usr/ports/biology/coverm/work/target/release/deps/libneedletail-1d31b72d7c5df58f.rlib --extern rayon=/wrkdirs/usr/ports/bio
logy/coverm/work/target/release/deps/librayon-d6ef5d92adf121bc.rmeta --extern skani=/wrkdirs/usr/ports/biology/coverm/work/target/release/deps/libskani-83fa282ce23cdda9.rmeta --extern tempfile=/wrkdirs/usr/ports/biology/coverm/work/target/release/deps/libtempfile-c76b3d3820cef404.rmeta --cap-lints warn -C target-cpu= -L native=/wrkdirs/usr/ports/biology/coverm/work/target/release/build/bzip2-sys-6bb7f267c18ddf84/out/lib -L native=/usr/lib`
error[E0308]: mismatched types
--> /wrkdirs/usr/ports/biology/coverm/work/CoverM-0.7.0/cargo-crates/rust-htslib-0.44.1/src/bam/record.rs:154:16
|
154 | l: sam_copy.len() as u64,
| ^^^^^^^^^^^^^^^^^^^^^ expected `u32`, found `u64`
error[E0308]: mismatched types
--> /wrkdirs/usr/ports/biology/coverm/work/CoverM-0.7.0/cargo-crates/rust-htslib-0.44.1/src/bam/record.rs:155:16
|
155 | m: sam_copy.len() as u64,
| ^^^^^^^^^^^^^^^^^^^^^ expected `u32`, found `u64`
error[E0308]: mismatched types
--> /wrkdirs/usr/ports/biology/coverm/work/CoverM-0.7.0/cargo-crates/rust-htslib-0.44.1/src/bam/mod.rs:179:21
|
177 | i64::from(htslib::cram_seek(
| ----------------- arguments to this function are incorrect
178 | htsfile.fp.cram,
179 | offset as libc::off_t,
| ^^^^^^^^^^^^^^^^^^^^^ expected `i32`, found `i64`
|
note: function defined here
--> /wrkdirs/usr/ports/biology/coverm/work/target/release/build/hts-sys-01897a4c42ff0bbf/out/bindings.rs:9704:12
|
9704 | pub fn cram_seek(
| ^^^^^^^^^
help: you can convert an `i64` to an `i32` and panic if the converted value doesn't fit
|
179 | (offset as libc::off_t).try_into().unwrap(),
| + +++++++++++++++++++++
error[E0308]: mismatched types
--> /wrkdirs/usr/ports/biology/coverm/work/CoverM-0.7.0/cargo-crates/rust-htslib-0.44.1/src/bam/mod.rs:1128:29
|
1128 | (*rec).l_text = l_text as u64;
| ------------- ^^^^^^^^^^^^^ expected `u32`, found `u64`
| |
| expected due to the type of this binding
error[E0308]: mismatched types
--> /wrkdirs/usr/ports/biology/coverm/work/CoverM-0.7.0/cargo-crates/rust-htslib-0.44.1/src/bam/mod.rs:1393:45
|
1393 | let rec = htslib::sam_hdr_parse((l_text + 1) as u64, text as *const c_char);
| --------------------- ^^^^^^^^^^^^^^^^^^^ expected `u32`, found `u64`
| |
| arguments to this function are incorrect
|
note: function defined here
--> /wrkdirs/usr/ports/biology/coverm/work/target/release/build/hts-sys-01897a4c42ff0bbf/out/bindings.rs:8520:12
|
8520 | pub fn sam_hdr_parse(l_text: size_t, text: *const ::std::os::raw::c_char) -> *mut sam_hdr_t;
| ^^^^^^^^^^^^^
help: you can convert a `u64` to a `u32` and panic if the converted value doesn't fit
|
1393 | let rec = htslib::sam_hdr_parse(((l_text + 1) as u64).try_into().unwrap(), text as *const c_char);
| + +++++++++++++++++++++
error[E0308]: mismatched types
--> /wrkdirs/usr/ports/biology/coverm/work/CoverM-0.7.0/cargo-crates/rust-htslib-0.44.1/src/bam/mod.rs:1395:29
|
1395 | (*rec).l_text = l_text as u64;
| ------------- ^^^^^^^^^^^^^ expected `u32`, found `u64`
| |
| expected due to the type of this binding
error[E0308]: mismatched types
--> /wrkdirs/usr/ports/biology/coverm/work/CoverM-0.7.0/cargo-crates/rust-htslib-0.44.1/src/bcf/record.rs:1011:48
|
1011 | let rm_set = unsafe { htslib::kbs_init(remove.len() as u64) };
| ---------------- ^^^^^^^^^^^^^^^^^^^ expected `u32`, found `u64`
| |
| arguments to this function are incorrect
|
note: function defined here
--> /wrkdirs/usr/ports/biology/coverm/work/target/release/build/hts-sys-01897a4c42ff0bbf/out/bindings.rs:11642:12
|
11642 | pub fn kbs_init(ni: size_t) -> *mut kbitset_t;
| ^^^^^^^^
help: you can convert a `u64` to a `u32` and panic if the converted value doesn't fit
|
1011 | let rm_set = unsafe { htslib::kbs_init((remove.len() as u64).try_into().unwrap()) };
| + +++++++++++++++++++++
error[E0308]: mismatched types
--> /wrkdirs/usr/ports/biology/coverm/work/CoverM-0.7.0/cargo-crates/rust-htslib-0.44.1/src/bgzf/mod.rs:118:17
|
115 | htslib::bgzf_read(
| ----------------- arguments to this function are incorrect
...
118 | buf.len() as u64,
| ^^^^^^^^^^^^^^^^ expected `u32`, found `u64`
|
note: function defined here
--> /wrkdirs/usr/ports/biology/coverm/work/target/release/build/hts-sys-01897a4c42ff0bbf/out/bindings.rs:10097:12
|
10097 | pub fn bgzf_read(fp: *mut BGZF, data: *mut ::std::os::raw::c_void, length: size_t) -> ssize_t;
| ^^^^^^^^^
help: you can convert a `u64` to a `u32` and panic if the converted value doesn't fit
|
118 | (buf.len() as u64).try_into().unwrap(),
| + +++++++++++++++++++++
error[E0308]: mismatched types
--> /wrkdirs/usr/ports/biology/coverm/work/CoverM-0.7.0/cargo-crates/rust-htslib-0.44.1/src/bgzf/mod.rs:264:17
|
261 | htslib::bgzf_write(
| ------------------ arguments to this function are incorrect
...
264 | buf.len() as u64,
| ^^^^^^^^^^^^^^^^ expected `u32`, found `u64`
|
note: function defined here
--> /wrkdirs/usr/ports/biology/coverm/work/target/release/build/hts-sys-01897a4c42ff0bbf/out/bindings.rs:10100:12
|
10100 | pub fn bgzf_write(
| ^^^^^^^^^^
help: you can convert a `u64` to a `u32` and panic if the converted value doesn't fit
|
264 | (buf.len() as u64).try_into().unwrap(),
| + +++++++++++++++++++++
For more information about this error, try `rustc --explain E0308`.
error: could not compile `rust-htslib` (lib) due to 9 previous errors
Caused by:
process didn't exit successfully: `CARGO=/usr/local/bin/cargo CARGO_CRATE_NAME=rust_htslib CARGO_MANIFEST_DIR=/wrkdirs/usr/ports/biology/coverm/work/CoverM-0.7.0/cargo-crates/rust-htslib-0.44.1 CARGO_MANIFEST_PATH=/wrkdirs/usr/ports/biology/coverm/work/CoverM-0.7.0/cargo-crates/rust-htslib-0.44.1/Cargo.toml CARGO_PKG_AUTHORS='Christopher Schröder <christopher.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 /u
sr/local/bin/rustc --crate-name rust_htslib --edition=2018 /wrkdirs/usr/ports/biology/coverm/work/CoverM-0.7.0/cargo-crates/rust-htslib-0.44.1/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C panic=abort -C linker-plugin-lto -C codegen-units=1 --check-cfg 'cfg(docsrs,test)' --check-cfg 'cfg(feature, values("bindgen", "bzip2", "curl", "default", "gcs", "libdeflate", "lzma", "s3", "serde", "serde_bytes", "serde_feature", "static"))' -C metadata=4f76b85ccc0f311d -C extra-filename=-c66c9e8616a92bc2 --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-43e822fa0dad2cfa.rmeta --extern byteorder=/wrkdirs/usr/ports/biology/coverm/work/target/release/deps/libbyteorder-b80956c97f283fcf.rme
ta --extern custom_derive=/wrkdirs/usr/ports/biology/coverm/work/target/release/deps/libcustom_derive-42ab22c6fd92b282.rmeta --extern derive_new=/wrkdirs/usr/ports/biology/coverm/work/target/release/deps/libderive_new-06696b8a7093e8c9.so --extern hts_sys=/wrkdirs/usr/ports/biology/coverm/work/target/release/deps/libhts_sys-c26ba8ec75b3dd26.rmeta --extern ieee754=/wrkdirs/usr/ports/biology/coverm/work/target/release/deps/libieee754-37ec808844007e98.rmeta --extern lazy_static=/wrkdirs/usr/ports/biology/coverm/work/target/release/deps/liblazy_static-94dbea200700be9c.rmeta --extern libc=/wrkdirs/usr/ports/biology/coverm/work/target/release/deps/liblibc-a6a7e02893365e9c.rmeta --extern linear_map=/wrkdirs/usr/ports/biology/coverm/work/target/release/deps/liblinear_map-2095da7606a15fa5.rmeta --extern newtype_derive=/wrkdirs/usr/ports/biology/coverm/work/target/release/deps/libnewtype_derive-d84c86f39cc705d8.rmeta --extern regex=/wrkdirs/usr/ports/biology/coverm/work/target/release/
deps/libregex-d0de2b51101d4bfd.rmeta --extern thiserror=/wrkdirs/usr/ports/biology/coverm/work/target/release/deps/libthiserror-ef7e45e6d240e6fa.rmeta --extern url=/wrkdirs/usr/ports/biology/coverm/work/target/release/deps/liburl-0cb3b73d39b7d724.rmeta --cap-lints warn -C target-cpu= -L native=/wrkdirs/usr/ports/biology/coverm/work/target/release/build/hts-sys-01897a4c42ff0bbf/out -L native=/wrkdirs/usr/ports/biology/coverm/work/target/release/build/libz-sys-8d49e24b54d2f48e/out/lib -L native=/wrkdirs/usr/ports/biology/coverm/work/target/release/build/libz-sys-8d49e24b54d2f48e/out/lib64` (exit status: 1)
warning: build failed, waiting for other jobs to finish...
warning: `skani` (lib) generated 3 warnings
*** Error code 101
Stop.
make: stopped in /usr/ports/biology/coverm