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Maintainer: [email protected] Log URL: https://pkg-status.freebsd.org/beefy24/data/main-amd64-default/pb14ef2e3a017_s1cc316727e/logs/haplohseq-0.1.2.3_2.log Build URL: https://pkg-status.freebsd.org/beefy24/build.html?mastername=main-amd64-default&build=pb14ef2e3a017_s1cc316727e Log: =>> Building biology/haplohseq build started at Wed Oct 22 00:00:40 -00 2025 port directory: /usr/ports/biology/haplohseq package name: haplohseq-0.1.2.3_2 building for: FreeBSD main-amd64-default-job-04 16.0-CURRENT FreeBSD 16.0-CURRENT 1600002 amd64 maintained by: [email protected] Makefile datestamp: -rw-r--r-- 1 root wheel 1174 Oct 21 01:01 /usr/ports/biology/haplohseq/Makefile Ports top last git commit: b14ef2e3a 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: 1600002 Job Id: 04 !!! Jail is newer than host. (Jail: 1600002, Host: 1600000) !!! !!! This is not supported. !!! !!! Host kernel must be same or newer than jail. !!! !!! Expect build failures. !!! ---Begin Environment--- SHELL=/bin/sh OSVERSION=1600002 UNAME_v=FreeBSD 16.0-CURRENT 1600002 UNAME_r=16.0-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=3.4.4 MASTERMNT=/usr/local/poudriere/data/.m/main-amd64-default/ref LC_COLLATE=C POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM=tmux-256color OUTPUT_REDIRECTED_STDERR=4 OUTPUT_REDIRECTED=1 PWD=/usr/local/poudriere/data/.m/main-amd64-default/04/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS MASTERNAME=main-amd64-default SCRIPTPREFIX=/usr/local/share/poudriere SCRIPTNAME=bulk.sh OLDPWD=/usr/local/poudriere/data/.m/main-amd64-default/ref/.p/pool POUDRIERE_PKGNAME=poudriere-git-3.4.4 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--- ===> 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-- [email protected] --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" --End CONFIGURE_ENV-- --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=freebsd16 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=16.0 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=freebsd16 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. #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) 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 [main-amd64-default-job-04] Installing pkg-2.3.1... [main-amd64-default-job-04] 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 [main-amd64-default-job-04] Installing gmake-4.4.1... [main-amd64-default-job-04] `-- Installing gettext-runtime-0.23.1... [main-amd64-default-job-04] | `-- Installing indexinfo-0.3.1_1... [main-amd64-default-job-04] | `-- Extracting indexinfo-0.3.1_1: .... done [main-amd64-default-job-04] `-- Extracting gettext-runtime-0.23.1: .......... done [main-amd64-default-job-04] 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 [main-amd64-default-job-04] Installing python311-3.11.14... [main-amd64-default-job-04] `-- Installing libffi-3.5.1... [main-amd64-default-job-04] `-- Extracting libffi-3.5.1: .......... done [main-amd64-default-job-04] `-- Installing mpdecimal-4.0.1... [main-amd64-default-job-04] `-- Extracting mpdecimal-4.0.1: .......... done [main-amd64-default-job-04] `-- Installing readline-8.2.13_2... [main-amd64-default-job-04] `-- Extracting readline-8.2.13_2: .......... done [main-amd64-default-job-04] 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 [main-amd64-default-job-04] Installing boost-libs-1.89.0... [main-amd64-default-job-04] `-- Installing icu-76.1,1... [main-amd64-default-job-04] `-- Extracting icu-76.1,1: .......... done [main-amd64-default-job-04] `-- Installing zstd-1.5.7... [main-amd64-default-job-04] | `-- Installing liblz4-1.10.0,1... [main-amd64-default-job-04] | `-- Extracting liblz4-1.10.0,1: .......... done [main-amd64-default-job-04] `-- Extracting zstd-1.5.7: .......... done [main-amd64-default-job-04] 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
