[package - 150releng-amd64-default][biology/haplohseq] Failed for haplohseq-0.1.2.3_2 in build
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Date: Tue, 21 Oct 2025 04:22:32 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: jwb@FreeBSD.org
Log URL: https://pkg-status.freebsd.org/beefy23/data/150releng-amd64-default/5beafd729224/logs/haplohseq-0.1.2.3_2.log
Build URL: https://pkg-status.freebsd.org/beefy23/build.html?mastername=150releng-amd64-default&build=5beafd729224
Log:
=>> Building biology/haplohseq
build started at Tue Oct 21 04:21:43 -00 2025
port directory: /usr/ports/biology/haplohseq
package name: haplohseq-0.1.2.3_2
building for: FreeBSD 150releng-amd64-default-job-21 15.0-BETA2 FreeBSD 15.0-BETA2 1500067 amd64
maintained by: jwb@FreeBSD.org
Makefile datestamp: -rw-r--r-- 1 root wheel 1174 Oct 21 01:01 /usr/ports/biology/haplohseq/Makefile
Ports top last git commit: 5beafd729
Ports top unclean checkout: no
Port dir last git commit: 67fb95fb3
Port dir unclean checkout: no
Poudriere version: poudriere-git-3.4.4
Host OSVERSION: 1600000
Jail OSVERSION: 1500067
Job Id: 21
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---Begin Poudriere Port Flags/Env---
PORT_FLAGS=
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FLAVOR=
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---End Poudriere Port Flags/Env---
---Begin OPTIONS List---
===> The following configuration options are available for haplohseq-0.1.2.3_2:
EXAMPLES=on: Build and/or install examples
===> Use 'make config' to modify these settings
---End OPTIONS List---
--MAINTAINER--
jwb@FreeBSD.org
--End MAINTAINER--
--CONFIGURE_ARGS--
--End CONFIGURE_ARGS--
--CONFIGURE_ENV--
MAKE=/usr/local/bin/gmake PYTHON="/usr/local/bin/python3.11" XDG_DATA_HOME=/wrkdirs/usr/ports/biology/haplohseq/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/haplohseq/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/haplohseq/work/.cache HOME=/wrkdirs/usr/ports/biology/haplohseq/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/haplohseq/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/haplohseq/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig SHELL=/bin/sh CONFIG_SHELL=/bin/sh CMAKE_PREFIX_PATH="/usr/local"
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--MAKE_ENV--
STRIP=-s XDG_DATA_HOME=/wrkdirs/usr/ports/biology/haplohseq/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/haplohseq/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/haplohseq/work/.cache HOME=/wrkdirs/usr/ports/biology/haplohseq/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/haplohseq/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/haplohseq/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 -isystem /usr/local/include -fno-strict-aliasing " CPP="cpp" CPPFLAGS="-isystem /usr/local/include" LDFLAGS=" -lpthread -L/usr/local/lib " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c++14 -isystem /usr/local/include " BSD_INSTAL
L_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--
PORTEXAMPLES="" PYTHON_INCLUDEDIR=include/python3.11 PYTHON_LIBDIR=lib/python3.11 PYTHON_PLATFORM=freebsd15 PYTHON_SITELIBDIR=lib/python3.11/site-packages PYTHON_SUFFIX=311 PYTHON_BASESUFFIX=311 PYTHON_TAG=.cpython-311 PYTHON_SOABI=.cpython-311 PYTHON_VER=3.11 PYTHON_BASEVER=3.11 PYTHON_VERSION=python3.11 PYTHON2="@comment " PYTHON3="" OSREL=15.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/haplohseq" EXAMPLESDIR="share/examples/haplohseq" DATADIR="share/haplohseq" WWWDIR="www/haplohseq" ETCDIR="etc/haplohseq"
--End PLIST_SUB--
--SUB_LIST--
PYTHON_INCLUDEDIR=/usr/local/include/python3.11 PYTHON_LIBDIR=/usr/local/lib/python3.11 PYTHON_PLATFORM=freebsd15 PYTHON_SITELIBDIR=/usr/local/lib/python3.11/site-packages PYTHON_SUFFIX=311 PYTHON_BASESUFFIX=311 PYTHON_TAG=.cpython-311 PYTHON_SOABI=.cpython-311 PYTHON_VER=3.11 PYTHON_BASEVER=3.11 PYTHON_VERSION=python3.11 PYTHON2="@comment " PYTHON3="" PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/haplohseq DOCSDIR=/usr/local/share/doc/haplohseq EXAMPLESDIR=/usr/local/share/examples/haplohseq WWWDIR=/usr/local/www/haplohseq ETCDIR=/usr/local/etc/haplohseq
--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.
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# 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) 33554432
stack size (kbytes, -s) 524288
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 MIT accepted by the user
===========================================================================
=======================<phase: pkg-depends >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===> haplohseq-0.1.2.3_2 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-2.3.1.pkg
[150releng-amd64-default-job-21] Installing pkg-2.3.1...
[150releng-amd64-default-job-21] Extracting pkg-2.3.1: .......... done
===> haplohseq-0.1.2.3_2 depends on file: /usr/local/sbin/pkg - found
===> Returning to build of haplohseq-0.1.2.3_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 MIT accepted by the user
===> Fetching all distfiles required by haplohseq-0.1.2.3_2 for building
===========================================================================
=======================<phase: checksum >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===> License MIT accepted by the user
===> Fetching all distfiles required by haplohseq-0.1.2.3_2 for building
=> SHA256 Checksum OK for outpaddling-haplohseq-0.1.2-3-gfeb9267_GH0.tar.gz.
===========================================================================
=======================<phase: extract-depends>============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===========================================================================
=======================<phase: extract >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===> License MIT accepted by the user
===> Fetching all distfiles required by haplohseq-0.1.2.3_2 for building
===> Extracting for haplohseq-0.1.2.3_2
=> SHA256 Checksum OK for outpaddling-haplohseq-0.1.2-3-gfeb9267_GH0.tar.gz.
===========================================================================
=======================<phase: patch-depends >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===========================================================================
=======================<phase: patch >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===> Patching for haplohseq-0.1.2.3_2
===========================================================================
=======================<phase: build-depends >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===> haplohseq-0.1.2.3_2 depends on package: gmake>=4.4.1 - not found
===> Installing existing package /packages/All/gmake-4.4.1.pkg
[150releng-amd64-default-job-21] Installing gmake-4.4.1...
[150releng-amd64-default-job-21] `-- Installing gettext-runtime-0.23.1...
[150releng-amd64-default-job-21] | `-- Installing indexinfo-0.3.1_1...
[150releng-amd64-default-job-21] | `-- Extracting indexinfo-0.3.1_1: .... done
[150releng-amd64-default-job-21] `-- Extracting gettext-runtime-0.23.1: .......... done
[150releng-amd64-default-job-21] Extracting gmake-4.4.1: .......... done
===> haplohseq-0.1.2.3_2 depends on package: gmake>=4.4.1 - found
===> Returning to build of haplohseq-0.1.2.3_2
===> haplohseq-0.1.2.3_2 depends on file: /usr/local/bin/python3.11 - not found
===> Installing existing package /packages/All/python311-3.11.14.pkg
[150releng-amd64-default-job-21] Installing python311-3.11.14...
[150releng-amd64-default-job-21] `-- Installing libffi-3.5.1...
[150releng-amd64-default-job-21] `-- Extracting libffi-3.5.1: .......... done
[150releng-amd64-default-job-21] `-- Installing mpdecimal-4.0.1...
[150releng-amd64-default-job-21] `-- Extracting mpdecimal-4.0.1: .......... done
[150releng-amd64-default-job-21] `-- Installing readline-8.2.13_2...
[150releng-amd64-default-job-21] `-- Extracting readline-8.2.13_2: .......... done
[150releng-amd64-default-job-21] Extracting python311-3.11.14: .......... done
=====
Message from python311-3.11.14:
--
Note that some standard Python modules are provided as separate ports
as they require additional dependencies. They are available as:
py311-gdbm databases/py-gdbm@py311
py311-sqlite3 databases/py-sqlite3@py311
py311-tkinter x11-toolkits/py-tkinter@py311
===> haplohseq-0.1.2.3_2 depends on file: /usr/local/bin/python3.11 - found
===> Returning to build of haplohseq-0.1.2.3_2
===========================================================================
=======================<phase: lib-depends >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===> haplohseq-0.1.2.3_2 depends on shared library: libboost_thread.so - not found
===> Installing existing package /packages/All/boost-libs-1.89.0.pkg
[150releng-amd64-default-job-21] Installing boost-libs-1.89.0...
[150releng-amd64-default-job-21] `-- Installing icu-76.1,1...
[150releng-amd64-default-job-21] `-- Extracting icu-76.1,1: .......... done
[150releng-amd64-default-job-21] `-- Installing zstd-1.5.7...
[150releng-amd64-default-job-21] | `-- Installing liblz4-1.10.0,1...
[150releng-amd64-default-job-21] | `-- Extracting liblz4-1.10.0,1: .......... done
[150releng-amd64-default-job-21] `-- Extracting zstd-1.5.7: .......... done
[150releng-amd64-default-job-21] Extracting boost-libs-1.89.0: .......... done
=====
Message from boost-libs-1.89.0:
--
You have built the Boost library with thread support.
Don't forget to add -pthread to your linker options when
linking your code.
===> haplohseq-0.1.2.3_2 depends on shared library: libboost_thread.so - found (/usr/local/lib/libboost_thread.so)
===> Returning to build of haplohseq-0.1.2.3_2
===========================================================================
=======================<phase: configure >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===> Configuring for haplohseq-0.1.2.3_2
===========================================================================
=======================<phase: build >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===> Building for haplohseq-0.1.2.3_2
mkdir -p build build/bin build/obj
mkdir -p build/test
c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c++14 -isystem /usr/local/include -I./src -I./src/hmm -I./src/util -isystem/usr/local/boost_1_52_0 -c -o build/obj/Hmm.o src/hmm/Hmm.cpp
cp -r src/test/resources build/test
c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c++14 -isystem /usr/local/include -I./src -I./src/hmm -I./src/util -isystem/usr/local/boost_1_52_0 -c -o build/obj/DataStructures.o src/hmm/DataStructures.cpp
c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c++14 -isystem /usr/local/include -I./src -I./src/hmm -I./src/util -isystem/usr/local/boost_1_52_0 -c -o build/obj/MathUtil.o src/hmm/MathUtil.cpp
c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c++14 -isystem /usr/local/include -I./src -I./src/hmm -I./src/util -isystem/usr/local/boost_1_52_0 -c -o build/obj/StringUtil.o src/util/StringUtil.cpp
c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c++14 -isystem /usr/local/include -I./src -I./src/hmm -I./src/util -isystem/usr/local/boost_1_52_0 -c -o build/obj/InputProcessor.o src/util/InputProcessor.cpp
src/util/StringUtil.cpp:51:76: warning: 'ptr_fun<int, int>' is deprecated [-Wdeprecated-declarations]
51 | s.erase(s.begin(), std::find_if(s.begin(), s.end(), std::not1(std::ptr_fun<int, int>(std::isspace))));
| ^
/usr/include/c++/v1/__functional/pointer_to_unary_function.h:35:1: note: 'ptr_fun<int, int>' has been explicitly marked deprecated here
35 | _LIBCPP_DEPRECATED_IN_CXX11 inline _LIBCPP_HIDE_FROM_ABI pointer_to_unary_function<_Arg, _Result>
| ^
/usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11'
736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
| ^
/usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED'
713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__))
| ^
src/util/StringUtil.cpp:57:67: warning: 'ptr_fun<int, int>' is deprecated [-Wdeprecated-declarations]
57 | s.erase(std::find_if(s.rbegin(), s.rend(), std::not1(std::ptr_fun<int, int>(std::isspace))).base(), s.end());
| ^
/usr/include/c++/v1/__functional/pointer_to_unary_function.h:35:1: note: 'ptr_fun<int, int>' has been explicitly marked deprecated here
35 | _LIBCPP_DEPRECATED_IN_CXX11 inline _LIBCPP_HIDE_FROM_ABI pointer_to_unary_function<_Arg, _Result>
| ^
/usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11'
736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
| ^
/usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED'
713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__))
| ^
2 warnings generated.
c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c++14 -isystem /usr/local/include -I./src -I./src/hmm -I./src/util -isystem/usr/local/boost_1_52_0 -c -o build/obj/Reporter.o src/Reporter.cpp
c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c++14 -isystem /usr/local/include -I./src -I./src/hmm -I./src/util -isystem/usr/local/boost_1_52_0 -c -o build/obj/FreqPhase.o src/FreqPhase.cpp
c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c++14 -isystem /usr/local/include -I./src -I./src/hmm -I./src/util -isystem/usr/local/boost_1_52_0 -c -o build/obj/VcfUtil.o src/util/VcfUtil.cpp
c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c++14 -isystem /usr/local/include -I./src -I./src/hmm -I./src/util -isystem/usr/local/boost_1_52_0 -c -o build/obj/HaplohSeq.o src/HaplohSeq.cpp
c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c++14 -isystem /usr/local/include -I./src -I./src/hmm -I./src/util -isystem/usr/local/boost_1_52_0 -isystem/usr/local/boost_1_52_0 -c -o build/test/FreqPhaseTest.o src/test/FreqPhaseTest.cpp
c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c++14 -isystem /usr/local/include -I./src -I./src/hmm -I./src/util -isystem/usr/local/boost_1_52_0 -isystem/usr/local/boost_1_52_0 -c -o build/test/HaplohSeqTest.o src/test/HaplohSeqTest.cpp
c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c++14 -isystem /usr/local/include -I./src -I./src/hmm -I./src/util -isystem/usr/local/boost_1_52_0 -isystem/usr/local/boost_1_52_0 -c -o build/test/HmmTest.o src/test/HmmTest.cpp
c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c++14 -isystem /usr/local/include -I./src -I./src/hmm -I./src/util -isystem/usr/local/boost_1_52_0 -isystem/usr/local/boost_1_52_0 -c -o build/test/InputProcessorTest.o src/test/InputProcessorTest.cpp
c++ -o build/bin/haplohseq -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -std=c++14 -isystem /usr/local/include -I./src -I./src/hmm -I./src/util -isystem/usr/local/boost_1_52_0 build/obj/Hmm.o build/obj/DataStructures.o build/obj/MathUtil.o build/obj/StringUtil.o build/obj/InputProcessor.o build/obj/Reporter.o build/obj/FreqPhase.o build/obj/VcfUtil.o build/obj/HaplohSeq.o -Llib/macosx -lm -lboost_program_options -lboost_system -lboost_filesystem -lboost_thread -lpthread -L/usr/local/lib
ld: error: unable to find library -lboost_system
c++: error: linker command failed with exit code 1 (use -v to see invocation)
gmake: *** [makefile:56: haplohseq] Error 1
gmake: *** Waiting for unfinished jobs....
===> Compilation failed unexpectedly.
Try to set MAKE_JOBS_UNSAFE=yes and rebuild before reporting the failure to
the maintainer.
*** Error code 1
Stop.
make: stopped making "build" in /usr/ports/biology/haplohseq