=>> Building biology/py-pywgsim build started at Mon Mar 16 19:06:24 EDT 2026 port directory: /usr/ports/biology/py-pywgsim package name: py311-pywgsim-0.5.2_2 building for: FreeBSD pkg.DaveG.ca 15.0-RELEASE-p3 FreeBSD 15.0-RELEASE-p3 1500068 amd64 maintained by: jwb@FreeBSD.org Makefile datestamp: -rw-r--r-- 1 root wheel 491 Mar 10 2025 /usr/ports/biology/py-pywgsim/Makefile Ports top last git commit: 8c988f802ea2 Ports top unclean checkout: no Port dir last git commit: 06a08e69f3ac Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.2 Host OSVERSION: 1500068 Jail OSVERSION: 1500068 Job Id: 05 ---Begin Environment--- SHELL=/bin/sh OSVERSION=1500068 UNAME_v=FreeBSD 15.0-RELEASE-p3 1500068 UNAME_r=15.0-RELEASE-p3 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/freebsd_15_0_x64-HEAD-ALL/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/freebsd_15_0_x64-HEAD-ALL/05/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS MASTERNAME=freebsd_15_0_x64-HEAD-ALL SCRIPTPREFIX=/usr/local/share/poudriere SCRIPTNAME=bulk.sh OLDPWD=/usr/local/poudriere/data/.m/freebsd_15_0_x64-HEAD-ALL/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=py311 MAKE_ARGS= FLAVOR=py311 ---End Poudriere Port Flags/Env--- ---Begin OPTIONS List--- ---End OPTIONS List--- --MAINTAINER-- jwb@FreeBSD.org --End MAINTAINER-- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- PYTHON="/usr/local/bin/python3.11" XDG_DATA_HOME=/wrkdirs/usr/ports/biology/py-pywgsim/work-py311 XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/py-pywgsim/work-py311 XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/py-pywgsim/work-py311/.cache HOME=/wrkdirs/usr/ports/biology/py-pywgsim/work-py311 TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/py-pywgsim/work-py311/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/py-pywgsim/work-py311/.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/py-pywgsim/work-py311 XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/py-pywgsim/work-py311 XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/py-pywgsim/work-py311/.cache HOME=/wrkdirs/usr/ports/biology/py-pywgsim/work-py311 TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/py-pywgsim/work-py311/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/py-pywgsim/work-py311/.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 LDSHARED="cc -shared" PYTHONDONTWRITEBYTECODE= PYTHONOPTIMIZE= 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-- 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/pywgsim" EXAMPLESDIR="share/examples/pywgsim" DATADIR="share/pywgsim" WWWDIR="www/pywgsim" ETCDIR="etc/pywgsim" --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/pywgsim DOCSDIR=/usr/local/share/doc/pywgsim EXAMPLESDIR=/usr/local/share/examples/pywgsim WWWDIR=/usr/local/www/pywgsim ETCDIR=/usr/local/etc/pywgsim --End SUB_LIST-- ---Begin make.conf--- DEFAULT_VERSIONS+=pgsql=15 DEFAULT_VERSIONS+=php=82 DISABLE_LICENSES=yes SELECTED_OPTIONS+=OPENBLAS ARCHDEF=AMD64K10h64SSE3 USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles FORCE_PACKAGE=yes PACKAGE_BUILDING=yes PACKAGE_BUILDING_FLAVORS=yes #### #### DEFAULT_VERSIONS+=pgsql=15 DEFAULT_VERSIONS+=php=82 DISABLE_LICENSES=yes SELECTED_OPTIONS+=OPENBLAS ARCHDEF=AMD64K10h64SSE3 WITH_CCACHE_BUILD=yes CCACHE_DIR=/root/.ccache #### 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-- =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> py311-pywgsim-0.5.2_2 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-2.6.2.pkg [pkg.DaveG.ca] Installing pkg-2.6.2... [pkg.DaveG.ca] Extracting pkg-2.6.2: .......... done ===> py311-pywgsim-0.5.2_2 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of py311-pywgsim-0.5.2_2 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by py311-pywgsim-0.5.2_2 for building =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by py311-pywgsim-0.5.2_2 for building => SHA256 Checksum OK for pywgsim-0.5.2.tar.gz. =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by py311-pywgsim-0.5.2_2 for building ===> Extracting for py311-pywgsim-0.5.2_2 => SHA256 Checksum OK for pywgsim-0.5.2.tar.gz. =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Patching for py311-pywgsim-0.5.2_2 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> py311-pywgsim-0.5.2_2 depends on package: py311-cython>=3.2.4 - not found ===> Installing existing package /packages/All/py311-cython-3.2.4.pkg [pkg.DaveG.ca] Installing py311-cython-3.2.4... [pkg.DaveG.ca] `-- Installing python311-3.11.15... [pkg.DaveG.ca] | `-- Installing gettext-runtime-0.26... [pkg.DaveG.ca] | | `-- Installing indexinfo-0.3.1_1... [pkg.DaveG.ca] | | `-- Extracting indexinfo-0.3.1_1: . done [pkg.DaveG.ca] | `-- Extracting gettext-runtime-0.26: .......... done [pkg.DaveG.ca] | `-- Installing libffi-3.5.1... [pkg.DaveG.ca] | `-- Extracting libffi-3.5.1: .......... done [pkg.DaveG.ca] | `-- Installing mpdecimal-4.0.1... [pkg.DaveG.ca] | `-- Extracting mpdecimal-4.0.1: .......... done [pkg.DaveG.ca] | `-- Installing readline-8.3.3... [pkg.DaveG.ca] | `-- Extracting readline-8.3.3: .......... done [pkg.DaveG.ca] `-- Extracting python311-3.11.15: .......... done [pkg.DaveG.ca] Extracting py311-cython-3.2.4: .......... done ===== Message from python311-3.11.15: -- 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 ===> py311-pywgsim-0.5.2_2 depends on package: py311-cython>=3.2.4 - found ===> Returning to build of py311-pywgsim-0.5.2_2 ===> py311-pywgsim-0.5.2_2 depends on package: py311-setuptools>=63.1.0 - not found ===> Installing existing package /packages/All/py311-setuptools-63.1.0_3.pkg [pkg.DaveG.ca] Installing py311-setuptools-63.1.0_3... [pkg.DaveG.ca] Extracting py311-setuptools-63.1.0_3: .......... done ===> py311-pywgsim-0.5.2_2 depends on package: py311-setuptools>=63.1.0 - found ===> Returning to build of py311-pywgsim-0.5.2_2 ===> py311-pywgsim-0.5.2_2 depends on file: /usr/local/bin/python3.11 - found ===> py311-pywgsim-0.5.2_2 depends on file: /usr/local/bin/ccache - not found ===> Installing existing package /packages/All/ccache-3.7.12_8.pkg [pkg.DaveG.ca] Installing ccache-3.7.12_8... [pkg.DaveG.ca] Extracting ccache-3.7.12_8: ......... done Create compiler links... create symlink for cc create symlink for cc (world) create symlink for c++ create symlink for c++ (world) create symlink for CC create symlink for CC (world) create symlink for clang create symlink for clang (world) create symlink for clang++ create symlink for clang++ (world) ===== Message from ccache-3.7.12_8: -- NOTE: Please read /usr/local/share/doc/ccache/ccache-howto-freebsd.txt for information on using ccache with FreeBSD ports and src. ===> py311-pywgsim-0.5.2_2 depends on file: /usr/local/bin/ccache - found ===> Returning to build of py311-pywgsim-0.5.2_2 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Configuring for py311-pywgsim-0.5.2_2 Compiling pywgsim/wgsim_lib.pyx because it changed. [1/1] Cythonizing pywgsim/wgsim_lib.pyx running config cython-3.11 /wrkdirs/usr/ports/biology/py-pywgsim/work-py311/pywgsim-0.5.2/pywgsim/wgsim_lib.pyx =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building for py311-pywgsim-0.5.2_2 running build running build_py creating build creating build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311 creating build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/pywgsim copying pywgsim/main.py -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/pywgsim copying pywgsim/__main__.py -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/pywgsim copying pywgsim/__init__.py -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/pywgsim running egg_info writing pywgsim.egg-info/PKG-INFO writing dependency_links to pywgsim.egg-info/dependency_links.txt writing entry points to pywgsim.egg-info/entry_points.txt writing requirements to pywgsim.egg-info/requires.txt writing top-level names to pywgsim.egg-info/top_level.txt reading manifest file 'pywgsim.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' writing manifest file 'pywgsim.egg-info/SOURCES.txt' /usr/local/lib/python3.11/site-packages/setuptools/command/build_py.py:153: SetuptoolsDeprecationWarning: Installing 'pywgsim.src' as data is deprecated, please list it in `packages`. !! ############################ # Package would be ignored # ############################ Python recognizes 'pywgsim.src' as an importable package, but it is not listed in the `packages` configuration of setuptools. 'pywgsim.src' has been automatically added to the distribution only because it may contain data files, but this behavior is likely to change in future versions of setuptools (and therefore is considered deprecated). Please make sure that 'pywgsim.src' is included as a package by using the `packages` configuration field or the proper discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" and "data files" on setuptools documentation page. !! check.warn(importable) copying pywgsim/wgsim_lib.c -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/pywgsim copying pywgsim/wgsim_lib.pyx -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/pywgsim creating build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/pywgsim/src copying pywgsim/src/Makefile -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/pywgsim/src copying pywgsim/src/kseq.h -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/pywgsim/src copying pywgsim/src/wgsim_mod.c -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/pywgsim/src copying pywgsim/src/wgsim_mod.h -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/pywgsim/src running build_ext building 'pywgsim.wgsim' extension creating build/temp.freebsd-15.0-RELEASE-p3-amd64-cpython-311 creating build/temp.freebsd-15.0-RELEASE-p3-amd64-cpython-311/pywgsim creating build/temp.freebsd-15.0-RELEASE-p3-amd64-cpython-311/pywgsim/src cc -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -Ipywgsim/src -I/usr/local/include/python3.11 -c pywgsim/src/wgsim_mod.c -o build/temp.freebsd-15.0-RELEASE-p3-amd64-cpython-311/pywgsim/src/wgsim_mod.o pywgsim/src/wgsim_mod.c:41:1: warning: comparison of integers of different signs: 'size_t' (aka 'unsigned long') and 'int' [-Wsign-compare] 41 | KSEQ_INIT(gzFile, gzread) | ^~~~~~~~~~~~~~~~~~~~~~~~~ pywgsim/src/kseq.h:220:2: note: expanded from macro 'KSEQ_INIT' 220 | KSTREAM_INIT(type_t, __read, 4096) \ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pywgsim/src/kseq.h:145:2: note: expanded from macro 'KSTREAM_INIT' 145 | __KS_GETUNTIL(__read, __bufsize) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pywgsim/src/kseq.h:120:24: note: expanded from macro '__KS_GETUNTIL' 120 | if (str->m - str->l < i - ks->begin + 1) { \ | ~~~~~~~~~~~~~~~ ^ ~~~~~~~~~~~~~~~~~ pywgsim/src/wgsim_mod.c:114:16: warning: comparison of integers of different signs: 'int' and 'const size_t' (aka 'const unsigned long') [-Wsign-compare] 114 | for (i = 0; i != ks->seq.l; ++i) { | ~ ^ ~~~~~~~~~ pywgsim/src/wgsim_mod.c:170:16: warning: comparison of integers of different signs: 'int' and 'const size_t' (aka 'const unsigned long') [-Wsign-compare] 170 | for (i = 0; i != ks->seq.l; ++i) { | ~ ^ ~~~~~~~~~ pywgsim/src/wgsim_mod.c:192:21: warning: comparison of integers of different signs: 'int' and 'const size_t' (aka 'const unsigned long') [-Wsign-compare] 192 | for (j = i; j < ks->seq.l && hap1->s[j] == hap2->s[j] && (hap1->s[j]&mutmsk) == DELETE; ++j) | ~ ^ ~~~~~~~~~ pywgsim/src/wgsim_mod.c:221:21: warning: comparison of integers of different signs: 'int' and 'const size_t' (aka 'const unsigned long') [-Wsign-compare] 221 | for (j = i; j < ks->seq.l && hap1->s[j] != hap2->s[j] && (hap1->s[j]&mutmsk) == DELETE; ++j) | ~ ^ ~~~~~~~~~ pywgsim/src/wgsim_mod.c:231:21: warning: comparison of integers of different signs: 'int' and 'const size_t' (aka 'const unsigned long') [-Wsign-compare] 231 | for (j = i; j < ks->seq.l && hap1->s[j] != hap2->s[j] && (hap2->s[j]&mutmsk) == DELETE; ++j) | ~ ^ ~~~~~~~~~ pywgsim/src/wgsim_mod.c:341:56: warning: comparison of integers of different signs: 'int' and 'size_t' (aka 'unsigned long') [-Wsign-compare] 341 | } while (pos < 0 || pos >= ks->seq.l || pos + d - 1 >= ks->seq.l); | ~~~~~~~~~~~ ^ ~~~~~~~~~ pywgsim/src/wgsim_mod.c:341:28: warning: comparison of integers of different signs: 'int' and 'size_t' (aka 'unsigned long') [-Wsign-compare] 341 | } while (pos < 0 || pos >= ks->seq.l || pos + d - 1 >= ks->seq.l); | ~~~ ^ ~~~~~~~~~ pywgsim/src/wgsim_mod.c:379:4: warning: comparison of integers of different signs: 'int' and 'size_t' (aka 'unsigned long') [-Wsign-compare] 379 | __gen_read(0, pos, ++i); | ^~~~~~~~~~~~~~~~~~~~~~~ pywgsim/src/wgsim_mod.c:358:61: note: expanded from macro '__gen_read' 358 | for (i = (start), k = 0, ext_coor[x] = -10; i >= 0 && i < ks->seq.l && k < s[x]; iter) { \ | ~ ^ ~~~~~~~~~ pywgsim/src/wgsim_mod.c:380:4: warning: comparison of integers of different signs: 'int' and 'size_t' (aka 'unsigned long') [-Wsign-compare] 380 | __gen_read(1, pos + d - 1, --i); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pywgsim/src/wgsim_mod.c:358:61: note: expanded from macro '__gen_read' 358 | for (i = (start), k = 0, ext_coor[x] = -10; i >= 0 && i < ks->seq.l && k < s[x]; iter) { \ | ~ ^ ~~~~~~~~~ 10 warnings generated. cc -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -Ipywgsim/src -I/usr/local/include/python3.11 -c pywgsim/wgsim_lib.c -o build/temp.freebsd-15.0-RELEASE-p3-amd64-cpython-311/pywgsim/wgsim_lib.o cc -shared -O2 -pipe -fstack-protector-strong -fno-strict-aliasing build/temp.freebsd-15.0-RELEASE-p3-amd64-cpython-311/pywgsim/src/wgsim_mod.o build/temp.freebsd-15.0-RELEASE-p3-amd64-cpython-311/pywgsim/wgsim_lib.o -L/usr/local/lib -lz -lm -o build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/pywgsim/wgsim.cpython-311.so =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> py311-pywgsim-0.5.2_2 depends on package: py311-plac>=0 - not found ===> Installing existing package /packages/All/py311-plac-1.4.3_1.pkg [pkg.DaveG.ca] Installing py311-plac-1.4.3_1... [pkg.DaveG.ca] `-- Installing py311-argparse-1.4.0_1... [pkg.DaveG.ca] `-- Extracting py311-argparse-1.4.0_1: ....... done [pkg.DaveG.ca] Extracting py311-plac-1.4.3_1: .......... done ===> py311-pywgsim-0.5.2_2 depends on package: py311-plac>=0 - found ===> Returning to build of py311-pywgsim-0.5.2_2 ===> py311-pywgsim-0.5.2_2 depends on file: /usr/local/bin/python3.11 - found =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Staging for py311-pywgsim-0.5.2_2 ===> Generating temporary packing list running install /usr/local/lib/python3.11/site-packages/setuptools/command/install.py:34: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools. warnings.warn( running build running build_py running egg_info writing pywgsim.egg-info/PKG-INFO writing dependency_links to pywgsim.egg-info/dependency_links.txt writing entry points to pywgsim.egg-info/entry_points.txt writing requirements to pywgsim.egg-info/requires.txt writing top-level names to pywgsim.egg-info/top_level.txt reading manifest file 'pywgsim.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' writing manifest file 'pywgsim.egg-info/SOURCES.txt' /usr/local/lib/python3.11/site-packages/setuptools/command/build_py.py:153: SetuptoolsDeprecationWarning: Installing 'pywgsim.src' as data is deprecated, please list it in `packages`. !! ############################ # Package would be ignored # ############################ Python recognizes 'pywgsim.src' as an importable package, but it is not listed in the `packages` configuration of setuptools. 'pywgsim.src' has been automatically added to the distribution only because it may contain data files, but this behavior is likely to change in future versions of setuptools (and therefore is considered deprecated). Please make sure that 'pywgsim.src' is included as a package by using the `packages` configuration field or the proper discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" and "data files" on setuptools documentation page. !! check.warn(importable) running build_ext running install_lib creating /wrkdirs/usr/ports/biology/py-pywgsim/work-py311/stage/usr/local/lib/python3.11 creating /wrkdirs/usr/ports/biology/py-pywgsim/work-py311/stage/usr/local/lib/python3.11/site-packages creating /wrkdirs/usr/ports/biology/py-pywgsim/work-py311/stage/usr/local/lib/python3.11/site-packages/pywgsim copying build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/pywgsim/main.py -> /wrkdirs/usr/ports/biology/py-pywgsim/work-py311/stage/usr/local/lib/python3.11/site-packages/pywgsim copying build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/pywgsim/__main__.py -> /wrkdirs/usr/ports/biology/py-pywgsim/work-py311/stage/usr/local/lib/python3.11/site-packages/pywgsim copying build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/pywgsim/__init__.py -> /wrkdirs/usr/ports/biology/py-pywgsim/work-py311/stage/usr/local/lib/python3.11/site-packages/pywgsim copying build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/pywgsim/wgsim_lib.c -> /wrkdirs/usr/ports/biology/py-pywgsim/work-py311/stage/usr/local/lib/python3.11/site-packages/pywgsim copying build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/pywgsim/wgsim_lib.pyx -> /wrkdirs/usr/ports/biology/py-pywgsim/work-py311/stage/usr/local/lib/python3.11/site-packages/pywgsim creating /wrkdirs/usr/ports/biology/py-pywgsim/work-py311/stage/usr/local/lib/python3.11/site-packages/pywgsim/src copying build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/pywgsim/src/wgsim_mod.c -> /wrkdirs/usr/ports/biology/py-pywgsim/work-py311/stage/usr/local/lib/python3.11/site-packages/pywgsim/src copying build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/pywgsim/src/wgsim_mod.h -> /wrkdirs/usr/ports/biology/py-pywgsim/work-py311/stage/usr/local/lib/python3.11/site-packages/pywgsim/src copying build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/pywgsim/src/Makefile -> /wrkdirs/usr/ports/biology/py-pywgsim/work-py311/stage/usr/local/lib/python3.11/site-packages/pywgsim/src copying build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/pywgsim/src/kseq.h -> /wrkdirs/usr/ports/biology/py-pywgsim/work-py311/stage/usr/local/lib/python3.11/site-packages/pywgsim/src copying build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/pywgsim/wgsim.cpython-311.so -> /wrkdirs/usr/ports/biology/py-pywgsim/work-py311/stage/usr/local/lib/python3.11/site-packages/pywgsim byte-compiling /wrkdirs/usr/ports/biology/py-pywgsim/work-py311/stage/usr/local/lib/python3.11/site-packages/pywgsim/main.py to main.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/py-pywgsim/work-py311/stage/usr/local/lib/python3.11/site-packages/pywgsim/__main__.py to __main__.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/py-pywgsim/work-py311/stage/usr/local/lib/python3.11/site-packages/pywgsim/__init__.py to __init__.cpython-311.pyc writing byte-compilation script '/tmp/tmpwyn9tf0f.py' /usr/local/bin/python3.11 /tmp/tmpwyn9tf0f.py removing /tmp/tmpwyn9tf0f.py running install_egg_info Copying pywgsim.egg-info to /wrkdirs/usr/ports/biology/py-pywgsim/work-py311/stage/usr/local/lib/python3.11/site-packages/pywgsim-0.5.2-py3.11.egg-info running install_scripts Installing pywgsim script to /wrkdirs/usr/ports/biology/py-pywgsim/work-py311/stage/usr/local/bin writing list of installed files to '/wrkdirs/usr/ports/biology/py-pywgsim/work-py311/.PLIST.pymodtmp' ====> Compressing man pages (compress-man) =========================================================================== =================================================== ===== env: 'PKG_NOTES=build_timestamp ports_top_git_hash ports_top_checkout_unclean port_git_hash port_checkout_unclean built_by' 'PKG_NOTE_build_timestamp=2026-03-16T23:06:24+0000' 'PKG_NOTE_ports_top_git_hash=8c988f802ea2' 'PKG_NOTE_ports_top_checkout_unclean=no' 'PKG_NOTE_port_git_hash=06a08e69f3ac' 'PKG_NOTE_port_checkout_unclean=no' 'PKG_NOTE_built_by=poudriere-git-3.4.2' NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building packages for py311-pywgsim-0.5.2_2 ===> Building py311-pywgsim-0.5.2_2 =========================================================================== =>> Cleaning up wrkdir ===> Cleaning for py311-pywgsim-0.5.2_2 build of biology/py-pywgsim@py311 | py311-pywgsim-0.5.2_2 ended at Mon Mar 16 19:07:30 EDT 2026 build time: 00:01:07