=>> Building biology/py-pywgsim build started at Sat Dec 4 05:48:28 MSK 2021 port directory: /usr/ports/biology/py-pywgsim package name: py311-pywgsim-0.5.2 building for: FreeBSD 13-amd64-default-py311-job-04 13.0-RELEASE-p4 FreeBSD 13.0-RELEASE-p4 amd64 maintained by: jwb@FreeBSD.org Makefile datestamp: -rw-r--r-- 1 root wheel 361 Sep 6 12:55 /usr/ports/biology/py-pywgsim/Makefile Poudriere version: poudriere-git-3.3.99.20211130 Host OSVERSION: 1300139 Jail OSVERSION: 1300139 Job Id: 04 ---Begin Environment--- SHELL=/bin/csh OSVERSION=1300139 UNAME_v=FreeBSD 13.0-RELEASE-p4 UNAME_r=13.0-RELEASE-p4 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 LOCALBASE=/usr/local USER=root POUDRIERE_NAME=poudriere-git LIBEXECPREFIX=/usr/local/libexec/poudriere POUDRIERE_VERSION=3.3.99.20211130 MASTERMNT=/usr/local/poudriere/data/.m/13-amd64-default-py311/ref LC_COLLATE=C POUDRIERE_BUILD_TYPE=bulk SAVED_TERM=screen GID=0 OUTPUT_REDIRECTED_STDERR=4 OUTPUT_REDIRECTED=1 UID=0 PWD=/usr/local/poudriere/data/.m/13-amd64-default-py311/04/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SELECTED_OPTIONS MASTERNAME=13-amd64-default-py311 SCRIPTPREFIX=/usr/local/share/poudriere SCRIPTNAME=bulk.sh OLDPWD=/usr/local/poudriere/data/.m/13-amd64-default-py311/ref/.p/pool POUDRIERE_PKGNAME=poudriere-git-3.3.99.20211130 SCRIPTPATH=/usr/local/share/poudriere/bulk.sh POUDRIEREPATH=/usr/local/bin/poudriere ---End Environment--- ---Begin Poudriere Port Flags/Env--- PORT_FLAGS= PKGENV= FLAVOR=py311 DEPENDS_ARGS= 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 PATH=/wrkdirs/usr/ports/biology/py-pywgsim/work-py311/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin 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 PATH=/wrkdirs/usr/ports/biology/py-pywgsim/work-py311/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin NO_PIE=yes 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=" -fstack-protector-strong " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " MANPREFIX="/usr/local" 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=freebsd13 PYTHON_SITELIBDIR=lib/python3.11/site-packages PYTHON_SUFFIX=311 PYTHON_EXT_SUFFIX=.cpython-311 PYTHON_VER=3.11 PYTHON_VERSION=python3.11 PYTHON2="@comment " PYTHON3="" OSREL=13.0 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-- 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--- USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles FORCE_PACKAGE=yes #### /usr/local/etc/poudriere.d/make.conf #### PETITECHEZ_AGREE_LICENSE= yes _LICENSE_STATUS= accepted #OPTIONS_UNSET+= DOXYGEN BOOTSTRAP OPTIONS_UNSET+= LATEX LTO BUILD_ALL_PYTHON_FLAVORS= yes .if ${.CURDIR:T} == "llvm11" || ${.CURDIR:T} == "llvm12" || ${.CURDIR:T} == "llvm13" || ${.CURDIR:T} == "gcc-arm-embedded" || ${.CURDIR:T} == "llvm-devel" || ${.CURDIR:T} == "llvm-cheri" BROKEN= no heavt crap from ports .endif #### /usr/local/etc/poudriere.d/py311-make.conf #### DEFAULT_VERSIONS+= python=3.11 python3=3.11 WITH_CCACHE_BUILD=yes CCACHE_DIR=/root/.ccache #### Misc Poudriere #### .include "/etc/make.conf.ports_env" ---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) 34275 open files (-n) 1024 virtual mem size (kbytes, -v) 4194304 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-- =================================================== ===== env: NO_DEPENDS=yes USER=nobody UID=65534 GID=65534 ===> License MIT accepted by the user =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> py311-pywgsim-0.5.2 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.17.5.pkg [13-amd64-default-py311-job-04] Installing pkg-1.17.5... [13-amd64-default-py311-job-04] Extracting pkg-1.17.5: .......... done ===> py311-pywgsim-0.5.2 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of py311-pywgsim-0.5.2 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> License MIT accepted by the user ===> Fetching all distfiles required by py311-pywgsim-0.5.2 for building =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> License MIT accepted by the user ===> Fetching all distfiles required by py311-pywgsim-0.5.2 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=nobody UID=65534 GID=65534 ===> License MIT accepted by the user ===> Fetching all distfiles required by py311-pywgsim-0.5.2 for building ===> Extracting for py311-pywgsim-0.5.2 => 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=nobody UID=65534 GID=65534 ===> Patching for py311-pywgsim-0.5.2 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> py311-pywgsim-0.5.2 depends on package: py311-setuptools>0 - not found ===> Installing existing package /packages/All/py311-setuptools-57.0.0.pkg [13-amd64-default-py311-job-04] Installing py311-setuptools-57.0.0... [13-amd64-default-py311-job-04] `-- Installing python311-3.11.0.a2... [13-amd64-default-py311-job-04] | `-- Installing gettext-runtime-0.21... [13-amd64-default-py311-job-04] | | `-- Installing indexinfo-0.3.1... [13-amd64-default-py311-job-04] | | `-- Extracting indexinfo-0.3.1: .... done [13-amd64-default-py311-job-04] | `-- Extracting gettext-runtime-0.21: .......... done [13-amd64-default-py311-job-04] | `-- Installing libffi-3.3_1... [13-amd64-default-py311-job-04] | `-- Extracting libffi-3.3_1: .......... done [13-amd64-default-py311-job-04] | `-- Installing mpdecimal-2.5.1... [13-amd64-default-py311-job-04] | `-- Extracting mpdecimal-2.5.1: .......... done [13-amd64-default-py311-job-04] | `-- Installing readline-8.1.1... [13-amd64-default-py311-job-04] | `-- Extracting readline-8.1.1: .......... done [13-amd64-default-py311-job-04] `-- Extracting python311-3.11.0.a2: .......... done [13-amd64-default-py311-job-04] Extracting py311-setuptools-57.0.0: .......... done ===== Message from python311-3.11.0.a2: -- 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 depends on package: py311-setuptools>0 - found ===> Returning to build of py311-pywgsim-0.5.2 ===> py311-pywgsim-0.5.2 depends on file: /usr/local/bin/python3.11 - found ===> py311-pywgsim-0.5.2 depends on file: /usr/local/bin/ccache - not found ===> Installing existing package /packages/All/ccache-3.7.12_2.pkg [13-amd64-default-py311-job-04] Installing ccache-3.7.12_2... [13-amd64-default-py311-job-04] Extracting ccache-3.7.12_2: .......... 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_2: -- 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 depends on file: /usr/local/bin/ccache - found ===> Returning to build of py311-pywgsim-0.5.2 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=nobody UID=65534 GID=65534 ===> Configuring for py311-pywgsim-0.5.2 running config =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=nobody UID=65534 GID=65534 ===> Building for py311-pywgsim-0.5.2 running build running build_py creating build creating build/lib.freebsd-13.0-RELEASE-p4-amd64-3.11 creating build/lib.freebsd-13.0-RELEASE-p4-amd64-3.11/pywgsim copying pywgsim/main.py -> build/lib.freebsd-13.0-RELEASE-p4-amd64-3.11/pywgsim copying pywgsim/__main__.py -> build/lib.freebsd-13.0-RELEASE-p4-amd64-3.11/pywgsim copying pywgsim/__init__.py -> build/lib.freebsd-13.0-RELEASE-p4-amd64-3.11/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' copying pywgsim/wgsim_lib.c -> build/lib.freebsd-13.0-RELEASE-p4-amd64-3.11/pywgsim copying pywgsim/wgsim_lib.pyx -> build/lib.freebsd-13.0-RELEASE-p4-amd64-3.11/pywgsim creating build/lib.freebsd-13.0-RELEASE-p4-amd64-3.11/pywgsim/src copying pywgsim/src/Makefile -> build/lib.freebsd-13.0-RELEASE-p4-amd64-3.11/pywgsim/src copying pywgsim/src/kseq.h -> build/lib.freebsd-13.0-RELEASE-p4-amd64-3.11/pywgsim/src copying pywgsim/src/wgsim_mod.c -> build/lib.freebsd-13.0-RELEASE-p4-amd64-3.11/pywgsim/src copying pywgsim/src/wgsim_mod.h -> build/lib.freebsd-13.0-RELEASE-p4-amd64-3.11/pywgsim/src running build_ext building 'pywgsim.wgsim' extension creating build/temp.freebsd-13.0-RELEASE-p4-amd64-3.11 creating build/temp.freebsd-13.0-RELEASE-p4-amd64-3.11/pywgsim creating build/temp.freebsd-13.0-RELEASE-p4-amd64-3.11/pywgsim/src cc -Wno-unused-result -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-13.0-RELEASE-p4-amd64-3.11/pywgsim/src/wgsim_mod.o pywgsim/src/wgsim_mod.c:41:1: warning: comparison of integers of different signs: 'unsigned long' and 'int' [-Wsign-compare] KSEQ_INIT(gzFile, gzread) ^~~~~~~~~~~~~~~~~~~~~~~~~ pywgsim/src/kseq.h:220:2: note: expanded from macro 'KSEQ_INIT' KSTREAM_INIT(type_t, __read, 4096) \ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pywgsim/src/kseq.h:145:2: note: expanded from macro 'KSTREAM_INIT' __KS_GETUNTIL(__read, __bufsize) ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pywgsim/src/kseq.h:120:24: note: expanded from macro '__KS_GETUNTIL' 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] 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] 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] 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] 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] 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] } 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] } 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] __gen_read(0, pos, ++i); ^~~~~~~~~~~~~~~~~~~~~~~ pywgsim/src/wgsim_mod.c:358:61: note: expanded from macro '__gen_read' 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] __gen_read(1, pos + d - 1, --i); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pywgsim/src/wgsim_mod.c:358:61: note: expanded from macro '__gen_read' for (i = (start), k = 0, ext_coor[x] = -10; i >= 0 && i < ks->seq.l && k < s[x]; iter) { \ ~ ^ ~~~~~~~~~ 10 warnings generated. cc -Wno-unused-result -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-13.0-RELEASE-p4-amd64-3.11/pywgsim/wgsim_lib.o pywgsim/wgsim_lib.c:220:12: fatal error: 'longintrepr.h' file not found #include "longintrepr.h" ^~~~~~~~~~~~~~~ 1 error generated. error: command '/usr/local/libexec/ccache/cc' failed with exit code 1 *** Error code 1 Stop. make: stopped in /usr/ports/biology/py-pywgsim =>> Cleaning up wrkdir ===> Cleaning for py311-pywgsim-0.5.2 build of biology/py-pywgsim@py311 | py311-pywgsim-0.5.2 ended at Sat Dec 4 05:48:43 MSK 2021 build time: 00:00:15 !!! build failure encountered !!!