[package - 141i386-default][biology/coverm] Failed for coverm-0.7.0 in build
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Date: Sun, 06 Oct 2024 01:33:10 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/beefy21/data/141i386-default/149fe86b8e79/logs/coverm-0.7.0.log
Build URL: https://pkg-status.freebsd.org/beefy21/build.html?mastername=141i386-default&build=149fe86b8e79
Log:
=>> Building biology/coverm
build started at Sun Oct 6 01:25:47 UTC 2024
port directory: /usr/ports/biology/coverm
package name: coverm-0.7.0
building for: FreeBSD 141i386-default-job-37 14.1-RELEASE-p5 FreeBSD 14.1-RELEASE-p5 i386
maintained by: yuri@FreeBSD.org
Makefile datestamp: -rw-r--r-- 1 root wheel 5628 Oct 6 01:01 /usr/ports/biology/coverm/Makefile
Ports top last git commit: 149fe86b8e
Ports top unclean checkout: no
Port dir last git commit: c4346c227e
Port dir unclean checkout: no
Poudriere version: poudriere-git-3.4.2
Host OSVERSION: 1500023
Jail OSVERSION: 1401000
Job Id: 37
---Begin Environment---
SHELL=/bin/sh
BLOCKSIZE=K
MAIL=/var/mail/root
MM_CHARSET=UTF-8
LANG=C.UTF-8
OSVERSION=1401000
STATUS=1
HOME=/root
PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin
MAKE_OBJDIR_CHECK_WRITABLE=0
UNAME_m=i386
UNAME_p=i386
UNAME_r=14.1-RELEASE-p5
LOCALBASE=/usr/local
UNAME_v=FreeBSD 14.1-RELEASE-p5
USER=root
POUDRIERE_NAME=poudriere-git
LIBEXECPREFIX=/usr/local/libexec/poudriere
POUDRIERE_VERSION=3.4.2
MASTERMNT=/usr/local/poudriere/data/.m/141i386-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/141i386-default/37/.p
OUTPUT_REDIRECTED_STDOUT=3
P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS
MASTERNAME=141i386-default
SCRIPTPREFIX=/usr/local/share/poudriere
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OLDPWD=/usr/local/poudriere/data/.m/141i386-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
MACHINE=i386
MACHINE_ARCH=i386
ARCH=${MACHINE_ARCH}
#### ####
# 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
DISABLE_MAKE_JOBS=poudriere
---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 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-1.21.3.pkg
[141i386-default-job-37] Installing pkg-1.21.3...
[141i386-default-job-37] 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
=> rust/crates/addr2line-0.24.2.crate doesn't seem to exist in /portdistfiles/.
=> Attempting to fetch https://crates.io/api/v1/crates/addr2line/0.24.2/download?dummy=/rust/crates/addr2line-0.24.2.crate
rust/crates/addr2line-0.24.2.crate 38 kB 4422 kBps 00s
=> rust/crates/assert_cli-0.6.3.crate doesn't seem to exist in /portdistfiles/.
=> Attempting to fetch https://crates.io/api/v1/crates/assert_cli/0.6.3/download?dummy=/rust/crates/assert_cli-0.6.3.crate
rust/crates/assert_cli-0.6.3.crate 18 kB 7371 kBps 00s
=> rust/crates/bio-types-1.0.4.crate doesn't seem to exist in /portdistfiles/.
=> Attempting to fetch https://crates.io/api/v1/crates/bio-types/1.0.4/download?dummy=/rust/crates/bio-types-1.0.4.crate
rust/crates/bio-types-1.0.4.crate 23 kB 4864 kBps 01s
=> rust/crates/bird_tool_utils-0.5.1.crate doesn't seem to exist in /portdistfiles/.
=> Attempting to fetch https://crates.io/api/v1/crates/bird_tool_utils/0.5.1/download?dummy=/rust/crates/bird_tool_utils-0.5.1.crate
rust/crates/bird_tool_utils-0.5.1.crate 6743 B 65 MBps 00s
=> rust/crates/bird_tool_utils-man-0.4.0.crate doesn't seem to exist in /portdistfiles/.
=> Attempting to fetch https://crates.io/api/v1/crates/bird_tool_utils-man/0.4.0/download?dummy=/rust/crates/bird_tool_utils-man-0.4.0.crate
rust/crates/bird_tool_utils-man-0.4.0.crate 16 kB 7159 kBps 00s
=> rust/crates/bit-vec-0.5.1.crate doesn't seem to exist in /portdistfiles/.
=> Attempting to fetch https://crates.io/api/v1/crates/bit-vec/0.5.1/download?dummy=/rust/crates/bit-vec-0.5.1.crate
rust/crates/bit-vec-0.5.1.crate 18 kB 8105 kBps 00s
=> rust/crates/buffer-redux-1.0.2.crate doesn't seem to exist in /portdistfiles/.
=> Attempting to fetch https://crates.io/api/v1/crates/buffer-redux/1.0.2/download?dummy=/rust/crates/buffer-redux-1.0.2.crate
rust/crates/buffer-redux-1.0.2.crate 25 kB 5845 kBps 00s
=> rust/crates/checkm-0.2.0.crate doesn't seem to exist in /portdistfiles/.
=> Attempting to fetch https://crates.io/api/v1/crates/checkm/0.2.0/download?dummy=/rust/crates/checkm-0.2.0.crate
rust/crates/checkm-0.2.0.crate 17 kB 5012 kBps 00s
=> rust/crates/disjoint-0.8.0.crate doesn't seem to exist in /portdistfiles/.
=> Attempting to fetch https://crates.io/api/v1/crates/disjoint/0.8.0/download?dummy=/rust/crates/disjoint-0.8.0.crate
rust/crates/disjoint-0.8.0.crate 17 kB 7571 kBps 00s
=> rust/crates/environment-0.1.1.crate doesn't seem to exist in /portdistfiles/.
=> Attempting to fetch https://crates.io/api/v1/crates/environment/0.1.1/download?dummy=/rust/crates/environment-0.1.1.crate
rust/crates/environment-0.1.1.crate 3227 B 28 MBps 00s
=> rust/crates/finch-0.6.0.crate doesn't seem to exist in /portdistfiles/.
=> Attempting to fetch https://crates.io/api/v1/crates/finch/0.6.0/download?dummy=/rust/crates/finch-0.6.0.crate
rust/crates/finch-0.6.0.crate 39 kB 4474 kBps 00s
=> rust/crates/fs-utils-1.1.4.crate doesn't seem to exist in /portdistfiles/.
=> Attempting to fetch https://crates.io/api/v1/crates/fs-utils/1.1.4/download?dummy=/rust/crates/fs-utils-1.1.4.crate
rust/crates/fs-utils-1.1.4.crate 3353 B 26 MBps 00s
=> rust/crates/galah-0.4.2.crate doesn't seem to exist in /portdistfiles/.
=> Attempting to fetch https://crates.io/api/v1/crates/galah/0.4.2/download?dummy=/rust/crates/galah-0.4.2.crate
rust/crates/galah-0.4.2.crate 828 kB 6560 kBps 00s
=> rust/crates/gbdt-0.1.3.crate doesn't seem to exist in /portdistfiles/.
=> Attempting to fetch https://crates.io/api/v1/crates/gbdt/0.1.3/download?dummy=/rust/crates/gbdt-0.1.3.crate
rust/crates/gbdt-0.1.3.crate 38 kB 4369 kBps 00s
=> rust/crates/gcollections-1.5.0.crate doesn't seem to exist in /portdistfiles/.
=> Attempting to fetch https://crates.io/api/v1/crates/gcollections/1.5.0/download?dummy=/rust/crates/gcollections-1.5.0.crate
rust/crates/gcollections-1.5.0.crate 16 kB 5039 kBps 00s
=> rust/crates/gimli-0.31.1.crate doesn't seem to exist in /portdistfiles/.
=> Attempting to fetch https://crates.io/api/v1/crates/gimli/0.31.1/download?dummy=/rust/crates/gimli-0.31.1.crate
rust/crates/gimli-0.31.1.crate 272 kB 3795 kBps 00s
<snip>
warning: trait objects without an explicit `dyn` are deprecated
--> /wrkdirs/usr/ports/biology/coverm/work/CoverM-0.7.0/cargo-crates/ansi_term-0.12.1/src/ansi.rs:308:21
|
308 | let f: &mut fmt::Write = f;
| ^^^^^^^^^^
|
= warning: this is accepted in the current edition (Rust 2015) but is a hard error in Rust 2021!
= note: for more information, see <https://doc.rust-lang.org/nightly/edition-guide/rust-2021/warnings-promoted-to-error.html>
help: if this is an object-safe trait, use `dyn`
|
308 | let f: &mut dyn fmt::Write = f;
| +++
warning: trait objects without an explicit `dyn` are deprecated
--> /wrkdirs/usr/ports/biology/coverm/work/CoverM-0.7.0/cargo-crates/ansi_term-0.12.1/src/display.rs:201:21
|
201 | let w: &mut fmt::Write = f;
| ^^^^^^^^^^
|
= warning: this is accepted in the current edition (Rust 2015) but is a hard error in Rust 2021!
= note: for more information, see <https://doc.rust-lang.org/nightly/edition-guide/rust-2021/warnings-promoted-to-error.html>
help: if this is an object-safe trait, use `dyn`
|
201 | let w: &mut dyn fmt::Write = f;
| +++
warning: trait objects without an explicit `dyn` are deprecated
--> /wrkdirs/usr/ports/biology/coverm/work/CoverM-0.7.0/cargo-crates/ansi_term-0.12.1/src/display.rs:210:21
|
210 | let w: &mut io::Write = w;
| ^^^^^^^^^
|
= warning: this is accepted in the current edition (Rust 2015) but is a hard error in Rust 2021!
= note: for more information, see <https://doc.rust-lang.org/nightly/edition-guide/rust-2021/warnings-promoted-to-error.html>
help: if this is an object-safe trait, use `dyn`
|
210 | let w: &mut dyn io::Write = w;
| +++
warning: trait objects without an explicit `dyn` are deprecated
--> /wrkdirs/usr/ports/biology/coverm/work/CoverM-0.7.0/cargo-crates/ansi_term-0.12.1/src/display.rs:229:21
|
229 | let f: &mut fmt::Write = f;
| ^^^^^^^^^^
|
= warning: this is accepted in the current edition (Rust 2015) but is a hard error in Rust 2021!
= note: for more information, see <https://doc.rust-lang.org/nightly/edition-guide/rust-2021/warnings-promoted-to-error.html>
help: if this is an object-safe trait, use `dyn`
|
229 | let f: &mut dyn fmt::Write = f;
| +++
warning: trait objects without an explicit `dyn` are deprecated
--> /wrkdirs/usr/ports/biology/coverm/work/CoverM-0.7.0/cargo-crates/ansi_term-0.12.1/src/display.rs:239:21
|
239 | let w: &mut io::Write = w;
| ^^^^^^^^^
|
= warning: this is accepted in the current edition (Rust 2015) but is a hard error in Rust 2021!
= note: for more information, see <https://doc.rust-lang.org/nightly/edition-guide/rust-2021/warnings-promoted-to-error.html>
help: if this is an object-safe trait, use `dyn`
|
239 | let w: &mut dyn io::Write = w;
| +++
warning: `ansi_term` (lib) generated 12 warnings
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_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,artifa
cts,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("nightly", "serde", "serde_impl", "serde_test"))' -C metadata=2724ae3934287d48 -C extra-filename=-2724ae3934287d48 --out-dir /wrkdirs/usr/ports/biology/coverm/work/target/i686-unknown-freebsd/release/deps --target i686-unknown-freebsd -C linker=cc -C strip=symbols -L dependency=/wrkdirs/usr/ports/biology/coverm/work/target/i686-unknown-freebsd/release/deps -L dependency=/wrkdirs/usr/ports/biology/coverm/work/target/release/deps --cap-lints warn -C link-arg=-fstack-protector-strong`
Compiling rust-htslib v0.44.1
Running `CARGO=/usr/local/bin/cargo CARGO_CRATE_NAME=rust_htslib CARGO_MANIFEST_DIR=/wrkdirs/usr/ports/biology/coverm/work/CoverM-0.7.0/cargo-crates/rust-htslib-0.44.1 CARGO_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=90253507f45a67e9 -C extra-filename=-90253507f45a67e9 --out-dir /wrkdirs/usr/ports/biology/coverm/work/target/i686-unknown-freebsd/release/deps --target i686-unknown-freebsd -C linker=cc -C strip=symbols -L dependency=/wrkdirs/usr/ports/biology/coverm/work/target/i686-unknown-freebsd/release/deps -L dependency=/wrkdirs/usr/ports/biology/coverm/work/target/release/deps --extern bio_types=/wrkdirs/usr/ports/biology/coverm/work/target/i686-unknown-freebsd/release/deps/libbio_types-44c12fb4de7402e2.rmeta --extern byteorder=/wrkdirs/usr/ports/biology/coverm/work/target/i686-unkno
wn-freebsd/release/deps/libbyteorder-029a8d1ccd35b272.rmeta --extern custom_derive=/wrkdirs/usr/ports/biology/coverm/work/target/i686-unknown-freebsd/release/deps/libcustom_derive-58c476ef2bf6a3c4.rmeta --extern derive_new=/wrkdirs/usr/ports/biology/coverm/work/target/release/deps/libderive_new-02d3faa64d5f6349.so --extern hts_sys=/wrkdirs/usr/ports/biology/coverm/work/target/i686-unknown-freebsd/release/deps/libhts_sys-d9bfe00b21217dea.rmeta --extern ieee754=/wrkdirs/usr/ports/biology/coverm/work/target/i686-unknown-freebsd/release/deps/libieee754-5536f4f364ae4e16.rmeta --extern lazy_static=/wrkdirs/usr/ports/biology/coverm/work/target/i686-unknown-freebsd/release/deps/liblazy_static-f710f21f93f27b06.rmeta --extern libc=/wrkdirs/usr/ports/biology/coverm/work/target/i686-unknown-freebsd/release/deps/liblibc-2f5eb096b76394c2.rmeta --extern linear_map=/wrkdirs/usr/ports/biology/coverm/work/target/i686-unknown-freebsd/release/deps/liblinear_map-2724ae3934287d48.rmeta --extern n
ewtype_derive=/wrkdirs/usr/ports/biology/coverm/work/target/i686-unknown-freebsd/release/deps/libnewtype_derive-b96113eeab79d790.rmeta --extern regex=/wrkdirs/usr/ports/biology/coverm/work/target/i686-unknown-freebsd/release/deps/libregex-b4e7efa46e75e7bf.rmeta --extern thiserror=/wrkdirs/usr/ports/biology/coverm/work/target/i686-unknown-freebsd/release/deps/libthiserror-38f0484651f1c454.rmeta --extern url=/wrkdirs/usr/ports/biology/coverm/work/target/i686-unknown-freebsd/release/deps/liburl-c0c87424d18528e8.rmeta --cap-lints warn -C link-arg=-fstack-protector-strong -L native=/wrkdirs/usr/ports/biology/coverm/work/target/i686-unknown-freebsd/release/build/hts-sys-c443e4bc928efde8/out -L native=/wrkdirs/usr/ports/biology/coverm/work/target/i686-unknown-freebsd/release/build/libz-sys-7cd1473bc4ead57a/out/lib -L native=/wrkdirs/usr/ports/biology/coverm/work/target/i686-unknown-freebsd/release/build/libz-sys-7cd1473bc4ead57a/out/lib64`
error[E0308]: mismatched types
--> /wrkdirs/usr/ports/biology/coverm/work/CoverM-0.7.0/cargo-crates/rust-htslib-0.44.1/src/bam/record.rs:154:16
|
154 | l: sam_copy.len() as u64,
| ^^^^^^^^^^^^^^^^^^^^^ expected `u32`, found `u64`
error[E0308]: mismatched types
--> /wrkdirs/usr/ports/biology/coverm/work/CoverM-0.7.0/cargo-crates/rust-htslib-0.44.1/src/bam/record.rs:155:16
|
155 | m: sam_copy.len() as u64,
| ^^^^^^^^^^^^^^^^^^^^^ expected `u32`, found `u64`
error[E0308]: mismatched types
--> /wrkdirs/usr/ports/biology/coverm/work/CoverM-0.7.0/cargo-crates/rust-htslib-0.44.1/src/bam/mod.rs:179:21
|
177 | i64::from(htslib::cram_seek(
| ----------------- arguments to this function are incorrect
178 | htsfile.fp.cram,
179 | offset as libc::off_t,
| ^^^^^^^^^^^^^^^^^^^^^ expected `i32`, found `i64`
|
note: function defined here
--> /wrkdirs/usr/ports/biology/coverm/work/target/i686-unknown-freebsd/release/build/hts-sys-c443e4bc928efde8/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/i686-unknown-freebsd/release/build/hts-sys-c443e4bc928efde8/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/i686-unknown-freebsd/release/build/hts-sys-c443e4bc928efde8/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/i686-unknown-freebsd/release/build/hts-sys-c443e4bc928efde8/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/i686-unknown-freebsd/release/build/hts-sys-c443e4bc928efde8/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_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=90253507f45a67e9 -C extra-filename=-90253507f45a67e9 --out-dir /wrkdirs/usr/ports/biology/coverm/work/target/i686-unknown-freebsd/release/deps --target i686-unknown-freebsd -C linker=cc -C strip=symbols -L dependency=/wrkdirs/usr/ports/biology/coverm/work/target/i686-unknown-freebsd/release/deps -L dependency=/wrkdirs/usr/ports/biology/coverm/work/target/release/deps --extern bio_types=/wrkdirs/usr/ports/biology/coverm/work/target/i686-unknown-freebsd/release/deps/libbio_types-44c12fb4de7402e2.rmeta --extern byteorder=/wrkdirs/usr/ports/biology/coverm
/work/target/i686-unknown-freebsd/release/deps/libbyteorder-029a8d1ccd35b272.rmeta --extern custom_derive=/wrkdirs/usr/ports/biology/coverm/work/target/i686-unknown-freebsd/release/deps/libcustom_derive-58c476ef2bf6a3c4.rmeta --extern derive_new=/wrkdirs/usr/ports/biology/coverm/work/target/release/deps/libderive_new-02d3faa64d5f6349.so --extern hts_sys=/wrkdirs/usr/ports/biology/coverm/work/target/i686-unknown-freebsd/release/deps/libhts_sys-d9bfe00b21217dea.rmeta --extern ieee754=/wrkdirs/usr/ports/biology/coverm/work/target/i686-unknown-freebsd/release/deps/libieee754-5536f4f364ae4e16.rmeta --extern lazy_static=/wrkdirs/usr/ports/biology/coverm/work/target/i686-unknown-freebsd/release/deps/liblazy_static-f710f21f93f27b06.rmeta --extern libc=/wrkdirs/usr/ports/biology/coverm/work/target/i686-unknown-freebsd/release/deps/liblibc-2f5eb096b76394c2.rmeta --extern linear_map=/wrkdirs/usr/ports/biology/coverm/work/target/i686-unknown-freebsd/release/deps/liblinear_map-2724ae3934
287d48.rmeta --extern newtype_derive=/wrkdirs/usr/ports/biology/coverm/work/target/i686-unknown-freebsd/release/deps/libnewtype_derive-b96113eeab79d790.rmeta --extern regex=/wrkdirs/usr/ports/biology/coverm/work/target/i686-unknown-freebsd/release/deps/libregex-b4e7efa46e75e7bf.rmeta --extern thiserror=/wrkdirs/usr/ports/biology/coverm/work/target/i686-unknown-freebsd/release/deps/libthiserror-38f0484651f1c454.rmeta --extern url=/wrkdirs/usr/ports/biology/coverm/work/target/i686-unknown-freebsd/release/deps/liburl-c0c87424d18528e8.rmeta --cap-lints warn -C link-arg=-fstack-protector-strong -L native=/wrkdirs/usr/ports/biology/coverm/work/target/i686-unknown-freebsd/release/build/hts-sys-c443e4bc928efde8/out -L native=/wrkdirs/usr/ports/biology/coverm/work/target/i686-unknown-freebsd/release/build/libz-sys-7cd1473bc4ead57a/out/lib -L native=/wrkdirs/usr/ports/biology/coverm/work/target/i686-unknown-freebsd/release/build/libz-sys-7cd1473bc4ead57a/out/lib64` (exit status: 1)
*** Error code 101
Stop.
make: stopped in /usr/ports/biology/coverm