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Maintainer: y...@freebsd.org Log URL: https://pkg-status.freebsd.org/ampere2/data/main-armv7-default/pd594ba044905_s6ea1ce222c/logs/coverm-0.7.0_2.log Build URL: https://pkg-status.freebsd.org/ampere2/build.html?mastername=main-armv7-default&build=pd594ba044905_s6ea1ce222c Log: =>> Building biology/coverm build started at Wed Jan 1 23:16:26 UTC 2025 port directory: /usr/ports/biology/coverm package name: coverm-0.7.0_2 building for: FreeBSD main-armv7-default-job-11 15.0-CURRENT FreeBSD 15.0-CURRENT 1500029 arm maintained by: y...@freebsd.org Makefile datestamp: -rw-r--r-- 1 root wheel 5806 Dec 19 01:01 /usr/ports/biology/coverm/Makefile Ports top last git commit: d594ba04490 Ports top unclean checkout: no Port dir last git commit: 39ac58d19ab Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.2 Host OSVERSION: 1500028 Jail OSVERSION: 1500029 Job Id: 11 !!! Jail is newer than host. (Jail: 1500029, Host: 1500028) !!! !!! This is not supported. !!! !!! Host kernel must be same or newer than jail. !!! !!! Expect build failures. !!! ---Begin Environment--- SHELL=/bin/sh OSVERSION=1500029 UNAME_v=FreeBSD 15.0-CURRENT 1500029 UNAME_r=15.0-CURRENT 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/main-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/main-armv7-default/11/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS MASTERNAME=main-armv7-default SCRIPTPREFIX=/usr/local/share/poudriere SCRIPTNAME=bulk.sh OLDPWD=/usr/local/poudriere/data/.m/main-armv7-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-- y...@freebsd.org --End MAINTAINER-- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- PKG_CONFIG=pkgconf XDG_DATA_HOME=/wrkdirs/usr/ports/biology/coverm/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/coverm/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/coverm/work/.cache HOME=/wrkdirs/usr/ports/biology/coverm/work TMPDIR="/wrkdirs/usr/ports/biology/coverm/work" PATH=/wrkdirs/usr/ports/biology/coverm/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/coverm/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig SHELL=/bin/sh CONFIG_SHELL=/bin/sh --End CONFIGURE_ENV-- --MAKE_ENV-- XDG_DATA_HOME=/wrkdirs/usr/ports/biology/coverm/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/coverm/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/coverm/work/.cache HOME=/wrkdirs/usr/ports/biology/coverm/work TMPDIR="/wrkdirs/usr/ports/biology/coverm/work" PATH=/wrkdirs/usr/ports/biology/coverm/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/coverm/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES PREFIX=/usr/local LOCALBASE=/usr/local CC="cc" CFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " CPP="cpp" CPPFLAGS="" LDFLAGS=" -fstack-protector-strong " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " BSD_INSTALL_PROGRAM="install -s -m 555" BSD_INSTALL_LIB="install -s -m 0644" BSD_INSTALL_SCRIPT="install -m 555" BSD_INSTA LL_DATA="install -m 0644" BSD_INSTALL_MAN="install -m 444" --End MAKE_ENV-- --PLIST_SUB-- OSREL=15.0 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 pipebuf (-y) 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_2 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.21.3.pkg [main-armv7-default-job-11] Installing pkg-1.21.3... [main-armv7-default-job-11] Extracting pkg-1.21.3: .......... done ===> coverm-0.7.0_2 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of coverm-0.7.0_2 =========================================================================== =======================<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_2 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_2 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. <snip> [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_MANIFEST_PATH=/wrkdirs/usr/ports/biology/coverm/work/CoverM-0.7.0/cargo-crates/hts-sys-2.1.4/Cargo.toml CARGO_PKG_AUTHORS='Christopher Schröder <christopher.schroe...@tu-dortmund.de>:Johannes Köster <johannes.koes...@tu-dortmund.de>' CARGO_PKG_DESCRIPTION='This library provides HTSlib bindings.' CARGO_PKG_HOMEPAGE='' CARGO_PKG_LICENSE=MIT CARGO_PKG_LICENSE_FILE='' CARGO_PKG_NAME=hts-sys CARGO_PKG_README=README.md CARGO_PKG_REPOSITORY='https://github.com/samtools/htslib.git' CARGO_PKG_RUST_VERSION='' CARGO_PKG_VERSION=2.1.4 CARGO_PKG_VERSION_MAJOR=2 CARGO_PKG_VERSION_MINOR=1 CARGO_PKG_VERSION_PATCH=4 CARGO_PKG_VERSION_PRE='' LD_LIBRARY_PATH=/wrkdirs/usr/ports/biology/coverm/work/target/release/deps OUT_DIR=/wrkdirs/usr/ports/biology/coverm/work/target/release/build/hts-sys-c3c4c7ccd37e0633/out /usr/local/bi n/rustc --crate-name hts_sys --edition=2018 /wrkdirs/usr/ports/biology/coverm/work/CoverM-0.7.0/cargo-crates/hts-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=42c8a8b28fc75707 -C extra-filename=-42c8a8b28fc75707 --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-5b80280c03b6a7f5.rmeta --cap-lints warn -C target-cpu= -C link-arg=-fstack-protector-strong -L native=/wrkdirs/usr/ports/biology/cov erm/work/target/release/build/hts-sys-c3c4c7ccd37e0633/out -l static=hts -L native=/wrkdirs/usr/ports/biology/coverm/work/target/release/build/libz-sys-02fc58be1fd98f4f/out/lib -L native=/wrkdirs/usr/ports/biology/coverm/work/target/release/build/libz-sys-02fc58be1fd98f4f/out/lib64` warning: fields `1` and `2` are never read --> /wrkdirs/usr/ports/biology/coverm/work/CoverM-0.7.0/cargo-crates/nix-0.26.4/src/sys/sendfile.rs:76:13 | 74 | struct SendfileHeaderTrailer<'a>( | --------------------- fields in this struct 75 | libc::sf_hdtr, 76 | Option<Vec<IoSlice<'a>>>, | ^^^^^^^^^^^^^^^^^^^^^^^^ 77 | Option<Vec<IoSlice<'a>>>, | ^^^^^^^^^^^^^^^^^^^^^^^^ | = help: consider removing these fields = note: `SendfileHeaderTrailer` has derived impls for the traits `Debug` and `Clone`, but these are intentionally ignored during dead code analysis note: the lint level is defined here --> /wrkdirs/usr/ports/biology/coverm/work/CoverM-0.7.0/cargo-crates/nix-0.26.4/src/lib.rs:48:9 | 48 | #![deny(unused)] | ^^^^^^ = note: `#[warn(dead_code)]` implied by `#[warn(unused)]` warning: `hts-sys` (lib) generated 1 warning (1 duplicate) 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.schroe...@tu-dortmund.de>:Johannes Köster <johannes.koes...@tu-dortmund.de>' CARGO_PKG_DESCRIPTION='This library provides HTSlib bindings and a high level Rust API for reading and writing BAM files.' CARGO_PKG_HOMEPAGE='' CARGO_PKG_LICENSE=MIT CARGO_PKG_LICENSE_FILE='' CARGO_PKG_NAME=rust-htslib CARGO_PKG_README=README.md CARGO_PKG_REPOSITORY='https://github.com/rust-bio/rust-htslib.git' CARGO_PKG_RUST_VERSION='' CARGO_PKG_VERSION=0.44.1 CARGO_PKG_VERSION_MAJOR=0 CARGO_PKG_VERSION_MINOR=44 CARGO_PKG_VERSION_PATCH=1 CARGO_PKG_VERSION_PRE='' LD_LIBRARY_PATH=/wrkdirs/usr/ports/biology/coverm/work/target/release/deps /usr/local/bin/rustc --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)' --check-cfg 'cfg(feature, values("bindgen", "bzip2", "curl", "default", "gcs", "libdeflate", "lzma", "s3", "serde", "serde_bytes", "serde_feature", "static"))' -C metadata=4f051a6230481ada -C extra-filename=-4f051a6230481ada --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-91c51ac43a6251ee.rmeta --extern byteorder=/wrkdirs/usr/ports/biology/coverm/work/target/release/deps/libbyteorder-dffaf63bde304cbc.rmeta --extern custom_derive=/w rkdirs/usr/ports/biology/coverm/work/target/release/deps/libcustom_derive-7483bb2affc966c7.rmeta --extern derive_new=/wrkdirs/usr/ports/biology/coverm/work/target/release/deps/libderive_new-fc98a8aeb89995c6.so --extern hts_sys=/wrkdirs/usr/ports/biology/coverm/work/target/release/deps/libhts_sys-42c8a8b28fc75707.rmeta --extern ieee754=/wrkdirs/usr/ports/biology/coverm/work/target/release/deps/libieee754-4d2bff9be3298f89.rmeta --extern lazy_static=/wrkdirs/usr/ports/biology/coverm/work/target/release/deps/liblazy_static-5dc051c9ad114269.rmeta --extern libc=/wrkdirs/usr/ports/biology/coverm/work/target/release/deps/liblibc-30a588b0b0b53017.rmeta --extern linear_map=/wrkdirs/usr/ports/biology/coverm/work/target/release/deps/liblinear_map-5b15060627a20503.rmeta --extern newtype_derive=/wrkdirs/usr/ports/biology/coverm/work/target/release/deps/libnewtype_derive-ada766d388787f5b.rmeta --extern regex=/wrkdirs/usr/ports/biology/coverm/work/target/release/deps/libregex-63f53b471a5f67 fa.rmeta --extern thiserror=/wrkdirs/usr/ports/biology/coverm/work/target/release/deps/libthiserror-ff044f47e89505df.rmeta --extern url=/wrkdirs/usr/ports/biology/coverm/work/target/release/deps/liburl-9b1c47af21a048cb.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-c3c4c7ccd37e0633/out -L native=/wrkdirs/usr/ports/biology/coverm/work/target/release/build/libz-sys-02fc58be1fd98f4f/out/lib -L native=/wrkdirs/usr/ports/biology/coverm/work/target/release/build/libz-sys-02fc58be1fd98f4f/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/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-c3c4c7ccd37e0633/out/bindings.rs:9439:12 | 9439 | pub fn bam_mods_query_type( | ^^^^^^^^^^^^^^^^^^^ 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-c3c4c7ccd37e0633/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-c3c4c7ccd37e0633/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-c3c4c7ccd37e0633/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-c3c4c7ccd37e0633/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-c3c4c7ccd37e0633/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`. warning: `rust-htslib` (lib) generated 1 warning (1 duplicate) error: could not compile `rust-htslib` (lib) due to 10 previous errors; 1 warning emitted 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.schroe...@tu-dortmund.de>:Johannes Köster <johannes.koes...@tu-dortmund.de>' CARGO_PKG_DESCRIPTION='This library provides HTSlib bindings and a high level Rust API for reading and writing BAM files.' CARGO_PKG_HOMEPAGE='' CARGO_PKG_LICENSE=MIT CARGO_PKG_LICENSE_FILE='' CARGO_PKG_NAME=rust-htslib CARGO_PKG_README=README.md CARGO_PKG_REPOSITORY='https://github.com/rust-bio/rust-htslib.git' CARGO_PKG_RUST_VERSION='' CARGO_PKG_VERSION=0.44.1 CARGO_PKG_VERSION_MAJOR=0 CARGO_PKG_VERSION_MINOR=44 CARGO_PKG_VERSION_PATCH=1 CARGO_PKG_VERSION_PRE='' LD_LIBRARY_PATH=/wrkdirs/usr/ports/biology/coverm/work/target/release/deps /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)' --check-cfg 'cfg(feature, values("bindgen", "bzip2", "curl", "default", "gcs", "libdeflate", "lzma", "s3", "serde", "serde_bytes", "serde_feature", "static"))' -C metadata=4f051a6230481ada -C extra-filename=-4f051a6230481ada --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-91c51ac43a6251ee.rmeta --extern byteorder=/wrkdirs/usr/ports/biology/coverm/work/target/release/deps/libbyteorder-dffaf63bde304cbc.rmeta -- extern custom_derive=/wrkdirs/usr/ports/biology/coverm/work/target/release/deps/libcustom_derive-7483bb2affc966c7.rmeta --extern derive_new=/wrkdirs/usr/ports/biology/coverm/work/target/release/deps/libderive_new-fc98a8aeb89995c6.so --extern hts_sys=/wrkdirs/usr/ports/biology/coverm/work/target/release/deps/libhts_sys-42c8a8b28fc75707.rmeta --extern ieee754=/wrkdirs/usr/ports/biology/coverm/work/target/release/deps/libieee754-4d2bff9be3298f89.rmeta --extern lazy_static=/wrkdirs/usr/ports/biology/coverm/work/target/release/deps/liblazy_static-5dc051c9ad114269.rmeta --extern libc=/wrkdirs/usr/ports/biology/coverm/work/target/release/deps/liblibc-30a588b0b0b53017.rmeta --extern linear_map=/wrkdirs/usr/ports/biology/coverm/work/target/release/deps/liblinear_map-5b15060627a20503.rmeta --extern newtype_derive=/wrkdirs/usr/ports/biology/coverm/work/target/release/deps/libnewtype_derive-ada766d388787f5b.rmeta --extern regex=/wrkdirs/usr/ports/biology/coverm/work/target/release/deps/ libregex-63f53b471a5f67fa.rmeta --extern thiserror=/wrkdirs/usr/ports/biology/coverm/work/target/release/deps/libthiserror-ff044f47e89505df.rmeta --extern url=/wrkdirs/usr/ports/biology/coverm/work/target/release/deps/liburl-9b1c47af21a048cb.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-c3c4c7ccd37e0633/out -L native=/wrkdirs/usr/ports/biology/coverm/work/target/release/build/libz-sys-02fc58be1fd98f4f/out/lib -L native=/wrkdirs/usr/ports/biology/coverm/work/target/release/build/libz-sys-02fc58be1fd98f4f/out/lib64` (exit status: 1) warning: build failed, waiting for other jobs to finish... warning: `nix` (lib) generated 11 warnings (1 duplicate) warning: `galah` (lib) generated 1 warning (1 duplicate) *** Error code 101 Stop. make: stopped making "build" in /usr/ports/biology/coverm
