[package - 135i386-default][biology/seqkit] Failed for seqkit-2.11.0_1 in build
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Date: Sat, 27 Dec 2025 09:36:50 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/beefy15/data/135i386-default/4374557c4263/logs/seqkit-2.11.0_1.log
Build URL: https://pkg-status.freebsd.org/beefy15/build.html?mastername=135i386-default&build=4374557c4263
Log:
=>> Building biology/seqkit
build started at Sat Dec 27 09:35:42 -00 2025
port directory: /usr/ports/biology/seqkit
package name: seqkit-2.11.0_1
building for: FreeBSD 135i386-default-job-13 13.5-RELEASE-p8 FreeBSD 13.5-RELEASE-p8 i386
maintained by: yuri@FreeBSD.org
Makefile datestamp: -rw-r--r-- 1 root wheel 767 Dec 16 01:03 /usr/ports/biology/seqkit/Makefile
Ports top last git commit: 4374557c4263a6f9ec70d71b4083790860006eb5
Ports top unclean checkout: no
Port dir last git commit: 75d873b56a7440351ea2bdf9e4a6017db3889f32
Port dir unclean checkout: no
Poudriere version: poudriere-git-3.4.4-15-g61aba751
Host OSVERSION: 1600000
Jail OSVERSION: 1305000
Job Id: 13
---Begin Environment---
SHELL=/bin/csh
BLOCKSIZE=K
MAIL=/var/mail/root
MM_CHARSET=UTF-8
LANG=C.UTF-8
OSVERSION=1305000
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=13.5-RELEASE-p8
LOCALBASE=/usr/local
UNAME_v=FreeBSD 13.5-RELEASE-p8
USER=root
POUDRIERE_NAME=poudriere-git
LIBEXECPREFIX=/usr/local/libexec/poudriere
POUDRIERE_VERSION=3.4.4-15-g61aba751
MASTERMNT=/usr/local/poudriere/data/.m/135i386-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/135i386-default/13/.p
OUTPUT_REDIRECTED_STDOUT=3
P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS
MASTERNAME=135i386-default
SCRIPTPREFIX=/usr/local/share/poudriere
SCRIPTNAME=bulk.sh
OLDPWD=/usr/local/poudriere/data/.m/135i386-default/ref/.p/pool
POUDRIERE_PKGNAME=poudriere-git-3.4.4-15-g61aba751
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--
XDG_DATA_HOME=/wrkdirs/usr/ports/biology/seqkit/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/seqkit/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/seqkit/work/.cache HOME=/wrkdirs/usr/ports/biology/seqkit/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/seqkit/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/seqkit/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/seqkit/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/seqkit/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/seqkit/work/.cache HOME=/wrkdirs/usr/ports/biology/seqkit/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/seqkit/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/seqkit/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/seqkit" EXAMPLESDIR="share/examples/seqkit" DATADIR="share/seqkit" WWWDIR="www/seqkit" ETCDIR="etc/seqkit"
--End PLIST_SUB--
--SUB_LIST--
PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/seqkit DOCSDIR=/usr/local/share/doc/seqkit EXAMPLESDIR=/usr/local/share/examples/seqkit WWWDIR=/usr/local/www/seqkit ETCDIR=/usr/local/etc/seqkit
--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
---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 MIT accepted by the user
===========================================================================
=======================<phase: pkg-depends >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===> seqkit-2.11.0_1 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-2.5.1.pkg
[135i386-default-job-13] Installing pkg-2.5.1...
[135i386-default-job-13] Extracting pkg-2.5.1: .......... done
===> seqkit-2.11.0_1 depends on file: /usr/local/sbin/pkg - found
===> Returning to build of seqkit-2.11.0_1
===========================================================================
=======================<phase: fetch-depends >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===> seqkit-2.11.0_1 depends on file: /usr/local/bin/go124 - not found
===> Installing existing package /packages/All/go124-1.24.11.pkg
[135i386-default-job-13] Installing go124-1.24.11...
[135i386-default-job-13] Extracting go124-1.24.11: .......... done
===> seqkit-2.11.0_1 depends on file: /usr/local/bin/go124 - found
===> Returning to build of seqkit-2.11.0_1
===========================================================================
=======================<phase: fetch >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===> License MIT accepted by the user
===> Fetching all distfiles required by seqkit-2.11.0_1 for building
===> Fetching github.com/shenwei356/seqkit/v2 dependencies
# get https://proxy.golang.org/git.sr.ht/~sbinet/gg/@v/v0.3.1.mod
# get https://proxy.golang.org/github.com/mattn/go-runewidth/@v/v0.0.14.mod
# get https://proxy.golang.org/github.com/%21vivid%21cortex/ewma/@v/v1.1.1.mod
# get https://proxy.golang.org/github.com/acarl005/stripansi/@v/v0.0.0-20180116102854-5a71ef0e047d.mod
# get https://proxy.golang.org/github.com/ajstarks/svgo/@v/v0.0.0-20211024235047-1546f124cd8b.mod
# get https://proxy.golang.org/github.com/araddon/dateparse/@v/v0.0.0-20210429162001-6b43995a97de.mod
# get https://proxy.golang.org/github.com/biogo/biogo/@v/v1.0.4.mod
# get https://proxy.golang.org/github.com/biogo/hts/@v/v1.4.4.mod
# get https://proxy.golang.org/github.com/botond-sipos/thist/@v/v1.1.0.mod
# get https://proxy.golang.org/github.com/cespare/xxhash/v2/@v/v2.1.2.mod
# get https://proxy.golang.org/github.com/cznic/sortutil/@v/v0.0.0-20181122101858-f5f958428db8.mod
# get https://proxy.golang.org/github.com/dsnet/compress/@v/v0.0.1.mod
# get https://proxy.golang.org/github.com/dustin/go-humanize/@v/v1.0.1.mod
# get https://proxy.golang.org/github.com/edsrzf/mmap-go/@v/v1.2.0.mod
# get https://proxy.golang.org/github.com/elliotwutingfeng/asciiset/@v/v0.0.0-20230602022725-51bbb787efab.mod
# get https://proxy.golang.org/github.com/fsnotify/fsnotify/@v/v1.5.4.mod
# get https://proxy.golang.org/github.com/go-fonts/liberation/@v/v0.3.0.mod
# get https://proxy.golang.org/github.com/go-latex/latex/@v/v0.0.0-20230307184459-12ec69307ad9.mod
# get https://proxy.golang.org/github.com/go-pdf/fpdf/@v/v0.6.0.mod
# get https://proxy.golang.org/github.com/golang/freetype/@v/v0.0.0-20170609003504-e2365dfdc4a0.mod
# get https://proxy.golang.org/github.com/google/uuid/@v/v1.6.0.mod
# get https://proxy.golang.org/github.com/iafan/cwalk/@v/v0.0.0-20210125030640-586a8832a711.mod
# get https://proxy.golang.org/github.com/inconshreveable/mousetrap/@v/v1.1.0.mod
# get https://proxy.golang.org/github.com/klauspost/compress/@v/v1.18.0.mod
# get https://proxy.golang.org/github.com/klauspost/pgzip/@v/v1.2.6.mod
# get https://proxy.golang.org/github.com/mattn/go-isatty/@v/v0.0.16.mod
# get https://proxy.golang.org/github.com/mattn/go-colorable/@v/v0.1.13.mod
# get https://proxy.golang.org/github.com/logrusorgru/aurora/@v/v2.0.3+incompatible.mod
# get https://proxy.golang.org/github.com/acarl005/stripansi/@v/v0.0.0-20180116102854-5a71ef0e047d.mod: 200 OK (0.644s)
# get https://proxy.golang.org/sumdb/sum.golang.org/supported
# get https://proxy.golang.org/github.com/logrusorgru/aurora/@v/v2.0.3+incompatible.mod: 200 OK (0.660s)
# get https://proxy.golang.org/sumdb/sum.golang.org/supported: 404 Not Found (0.019s)
# get https://sum.golang.org/lookup/github.com/acarl005/stripansi@v0.0.0-20180116102854-5a71ef0e047d
# get https://sum.golang.org/lookup/github.com/logrusorgru/aurora@v2.0.3+incompatible
# get https://proxy.golang.org/github.com/go-latex/latex/@v/v0.0.0-20230307184459-12ec69307ad9.mod: 200 OK (0.717s)
# get https://sum.golang.org/lookup/github.com/go-latex/latex@v0.0.0-20230307184459-12ec69307ad9
# get https://proxy.golang.org/github.com/go-pdf/fpdf/@v/v0.6.0.mod: 200 OK (0.717s)
# get https://sum.golang.org/lookup/github.com/go-pdf/fpdf@v0.6.0
# get https://proxy.golang.org/github.com/mattn/go-colorable/@v/v0.1.13.mod: 200 OK (0.716s)
# get https://sum.golang.org/lookup/github.com/mattn/go-colorable@v0.1.13
# get https://proxy.golang.org/github.com/klauspost/compress/@v/v1.18.0.mod: 200 OK (0.716s)
<snip>
github.com/biogo/hts/bam
golang.org/x/image/font
golang.org/x/text/transform
golang.org/x/image/vector
golang.org/x/text/encoding
golang.org/x/text/encoding/internal
embed
golang.org/x/text/encoding/charmap
github.com/go-fonts/liberation/liberationmonobold
github.com/go-fonts/liberation/liberationmonobolditalic
github.com/go-fonts/liberation/liberationmonoitalic
github.com/go-fonts/liberation/liberationmonoregular
github.com/go-fonts/liberation/liberationsansbold
github.com/go-fonts/liberation/liberationsansbolditalic
github.com/go-fonts/liberation/liberationsansitalic
github.com/go-fonts/liberation/liberationsansregular
github.com/go-fonts/liberation/liberationserifbold
github.com/go-fonts/liberation/liberationserifbolditalic
github.com/go-fonts/liberation/liberationserifitalic
github.com/go-fonts/liberation/liberationserifregular
github.com/go-latex/latex/internal/tex2unicode
go/token
golang.org/x/image/font/sfnt
github.com/go-latex/latex/token
github.com/go-latex/latex/ast
text/scanner
github.com/go-latex/latex
golang.org/x/image/font/opentype
github.com/go-latex/latex/drawtex
github.com/go-latex/latex/mtex/symbols
gonum.org/v1/plot/font
github.com/go-latex/latex/font/ttf
gonum.org/v1/plot/font/liberation
github.com/go-latex/latex/tex
log/syslog
gonum.org/v1/plot/vg
github.com/shenwei356/go-logging
github.com/go-latex/latex/mtex
github.com/golang/freetype/raster
golang.org/x/image/draw
github.com/golang/freetype/truetype
gonum.org/v1/plot/text
gonum.org/v1/plot/vg/draw
gonum.org/v1/plot/vg/vgeps
golang.org/x/image/font/basicfont
image/jpeg
hash/adler32
io/ioutil
compress/zlib
image/png
golang.org/x/image/ccitt
golang.org/x/image/tiff/lzw
golang.org/x/image/tiff
crypto/rc4
crypto/internal/fips140/aes/gcm
internal/saferio
encoding/gob
crypto/cipher
git.sr.ht/~sbinet/gg
crypto/internal/boring
crypto/sha1
encoding/base64
encoding/json
gonum.org/v1/plot/vg/vgimg
encoding/xml
compress/lzw
image/gif
math/rand
html
gonum.org/v1/plot/vg/vgtex
runtime/debug
gonum.org/v1/plot/palette
github.com/go-pdf/fpdf
github.com/ajstarks/svgo
gonum.org/v1/plot/tools/bezier
github.com/cespare/xxhash/v2
math/big
gonum.org/v1/plot/vg/vgsvg
github.com/dsnet/compress/internal/errors
github.com/dsnet/compress
github.com/dsnet/compress/internal/prefix
github.com/dsnet/compress/bzip2
github.com/fsnotify/fsnotify
database/sql/driver
github.com/iafan/cwalk
github.com/klauspost/compress/fse
github.com/cznic/sortutil
github.com/dustin/go-humanize
crypto/rand
github.com/google/uuid
github.com/klauspost/compress/internal/le
github.com/klauspost/compress/huff0
github.com/klauspost/compress/internal/snapref
github.com/klauspost/compress/zstd/internal/xxhash
github.com/klauspost/compress/flate
gonum.org/v1/plot/vg/vgpdf
github.com/klauspost/compress/zstd
gonum.org/v1/plot
gonum.org/v1/plot/plotter
github.com/klauspost/pgzip
github.com/logrusorgru/aurora
os/exec
gonum.org/v1/plot/plotutil
github.com/mitchellh/go-homedir
github.com/botond-sipos/thist
github.com/pkg/errors
crypto/sha256
github.com/ulikunitz/xz/internal/xlog
hash/crc64
crypto/aes
crypto/des
github.com/ulikunitz/xz/lzma
# github.com/ulikunitz/xz/lzma
vendor/github.com/ulikunitz/xz/lzma/reader.go:33:15: cannot use 1 << 31 (untyped int constant 2147483648) as int value in assignment (overflows)
crypto/internal/fips140/edwards25519/field
crypto/internal/fips140/nistec/fiat
crypto/internal/boring/bbig
crypto/internal/impl
crypto/internal/fips140/bigmod
crypto/sha3
crypto/internal/fips140hash
crypto/sha512
encoding/asn1
crypto/internal/fips140/edwards25519
crypto/internal/fips140/ed25519
crypto/ed25519
crypto/hmac
vendor/golang.org/x/crypto/cryptobyte
crypto/internal/fips140/hkdf
crypto/internal/fips140/mlkem
crypto/internal/fips140/tls12
crypto/internal/fips140/tls13
vendor/golang.org/x/crypto/chacha20
vendor/golang.org/x/crypto/internal/poly1305
crypto/internal/fips140/rsa
vendor/golang.org/x/crypto/chacha20poly1305
crypto/tls/internal/fips140tls
crypto/dsa
crypto/internal/fips140/nistec
crypto/x509/pkix
crypto/rsa
encoding/pem
vendor/golang.org/x/text/transform
vendor/golang.org/x/text/unicode/bidi
vendor/golang.org/x/text/unicode/norm
vendor/golang.org/x/text/secure/bidirule
net/textproto
vendor/golang.org/x/net/http2/hpack
crypto/internal/fips140/ecdh
crypto/ecdh
crypto/elliptic
crypto/internal/fips140/ecdsa
crypto/internal/hpke
vendor/golang.org/x/net/idna
mime
crypto/ecdsa
vendor/golang.org/x/net/http/httpguts
vendor/golang.org/x/net/http/httpproxy
mime/quotedprintable
net/http/internal
mime/multipart
net/http/internal/ascii
os/user
crypto/x509
github.com/twotwotwo/sorts
github.com/twotwotwo/sorts/sortutil
github.com/shenwei356/util/byteutil
github.com/shenwei356/bio/seq
github.com/edsrzf/mmap-go
github.com/shenwei356/bio/seqio/fai
github.com/shenwei356/bio/util
index/suffixarray
github.com/mattn/go-runewidth
crypto/tls
github.com/shenwei356/stable
github.com/shenwei356/bwt
github.com/shenwei356/util/pathutil
github.com/araddon/dateparse
github.com/shenwei356/bwt/fmi
github.com/shenwei356/natsort
gopkg.in/yaml.v2
github.com/shenwei356/util/stringutil
encoding/csv
flag
github.com/spf13/pflag
github.com/smallfish/simpleyaml
text/template/parse
github.com/acarl005/stripansi
github.com/vbauerster/mpb/v5/cwriter
github.com/vbauerster/mpb/v5/decor
text/template
github.com/vbauerster/mpb/v5
net/http/httptrace
os/signal
net/http
github.com/spf13/cobra
*** Error code 1
Stop.
make: stopped in /usr/ports/biology/seqkit