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Maintainer: [email protected] Log URL: https://pkg-status.freebsd.org/ampere3/data/144arm64-default/09cb03cda62d/logs/vcftools-0.1.17.log Build URL: https://pkg-status.freebsd.org/ampere3/build.html?mastername=144arm64-default&build=09cb03cda62d Log: =>> Building biology/vcftools build started at Sun Aug 30 18:25:49 UTC 2026 port directory: /usr/ports/biology/vcftools package name: vcftools-0.1.17 building for: FreeBSD 144arm64-default-job-03 14.4-RELEASE-p9 FreeBSD 14.4-RELEASE-p9 arm64 maintained by: [email protected] Makefile datestamp: -rw-r--r-- 1 root wheel 419 Jun 14 2025 /usr/ports/biology/vcftools/Makefile Ports top last git commit: 09cb03cda62da1fcd6c53c385d2997ae6d53ca1f Ports top unclean checkout: no Port dir last git commit: 3ae8b09ca041e222fc171fa7aad9ea44eab03484 Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.8-2-g2e891d4a Host OSVERSION: 1600019 Jail OSVERSION: 1404000 Job Id: 03 ---Begin Environment--- SHELL=/bin/sh OSVERSION=1404000 UNAME_v=FreeBSD 14.4-RELEASE-p9 UNAME_r=14.4-RELEASE-p9 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=3.4.8-2-g2e891d4a MASTERMNT=/usr/local/poudriere/data/.m/144arm64-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/144arm64-default/03/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS MASTERNAME=144arm64-default SCRIPTPREFIX=/usr/local/share/poudriere SCRIPTNAME=bulk.sh OLDPWD=/usr/local/poudriere/data/.m/144arm64-default/ref/.p/pool POUDRIERE_PKGNAME=poudriere-git-3.4.8-2-g2e891d4a 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-- [email protected] --End MAINTAINER-- --CONFIGURE_ARGS-- --prefix=/usr/local ${_LATE_CONFIGURE_ARGS} --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- MAKE=/usr/local/bin/gmake ac_cv_path_PERL=/usr/local/bin/perl ac_cv_path_PERL_PATH=/usr/local/bin/perl PERL_USE_UNSAFE_INC=1 PKG_CONFIG=pkgconf XDG_DATA_HOME=/wrkdirs/usr/ports/biology/vcftools/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/vcftools/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/vcftools/work/.cache HOME=/wrkdirs/usr/ports/biology/vcftools/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/vcftools/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/vcftools/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig SHELL=/bin/sh CONFIG_SHELL=/bin/sh DEFAULT_AUTOCONF=2.73 CONFIG_SITE=/usr/ports/Templates/config.site lt_cv_sys_max_cmd_len=524288 --End CONFIGURE_ENV-- --MAKE_ENV-- PERL_USE_UNSAFE_INC=1 XDG_DATA_HOME=/wrkdirs/usr/ports/biology/vcftools/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/vcftools/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/vcftools/work/.cache HOME=/wrkdirs/usr/ports/biology/vcftools/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/vcftools/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/vcftools/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 DEFAULT_AUTOCONF=2.73 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 -std=c++14 " BSD_INSTALL_PROGRAM="install -s -m 555" BSD_INSTALL_LIB="install -s -m 0644" BSD_INSTALL_SCRIPT="install -m 555" B SD_INSTALL_DATA="install -m 0644" BSD_INSTALL_MAN="install -m 444" --End MAKE_ENV-- --PLIST_SUB-- OSREL=14.4 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib PERL_VERSION=5.42.3 PERL_VER=5.42 PERL5_MAN1=lib/perl5/site_perl/man/man1 PERL5_MAN3=lib/perl5/site_perl/man/man3 SITE_PERL=lib/perl5/site_perl SITE_ARCH=lib/perl5/site_perl/mach/5.42 DOCSDIR="share/doc/vcftools" EXAMPLESDIR="share/examples/vcftools" DATADIR="share/vcftools" WWWDIR="www/vcftools" ETCDIR="etc/vcftools" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/vcftools DOCSDIR=/usr/local/share/doc/vcftools EXAMPLESDIR=/usr/local/share/examples/vcftools WWWDIR=/usr/local/www/vcftools ETCDIR=/usr/local/etc/vcftools --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 #### #### # 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) 1048576 stack size (kbytes, -s) 1048576 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 LGPL3 accepted by the user =========================================================================== =======================<phase: pkg-depends >============================ ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> vcftools-0.1.17 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-2.8.4.pkg [144arm64-default-job-03] Installing pkg-2.8.4... [144arm64-default-job-03] Extracting pkg-2.8.4: .......... done ===> vcftools-0.1.17 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of vcftools-0.1.17 =========================================================================== =======================<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 LGPL3 accepted by the user ===> Fetching all distfiles required by vcftools-0.1.17 for building =========================================================================== =======================<phase: checksum >============================ ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> License LGPL3 accepted by the user ===> Fetching all distfiles required by vcftools-0.1.17 for building => SHA256 Checksum OK for vcftools-vcftools-v0.1.17_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 LGPL3 accepted by the user ===> Fetching all distfiles required by vcftools-0.1.17 for building ===> Extracting for vcftools-0.1.17 => SHA256 Checksum OK for vcftools-vcftools-v0.1.17_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 vcftools-0.1.17 =========================================================================== =======================<phase: build-depends >============================ ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> vcftools-0.1.17 depends on package: gmake>=4.4.1 - not found ===> Installing existing package /packages/All/gmake-4.4.1.pkg [144arm64-default-job-03] Installing gmake-4.4.1... [144arm64-default-job-03] `-- Installing gettext-runtime-1.0_1... [144arm64-default-job-03] | `-- Installing indexinfo-0.3.1_1... [144arm64-default-job-03] | `-- Extracting indexinfo-0.3.1_1: .... done [144arm64-default-job-03] `-- Extracting gettext-runtime-1.0_1: .......... done [144arm64-default-job-03] Extracting gmake-4.4.1: .......... done ===> vcftools-0.1.17 depends on package: gmake>=4.4.1 - found ===> Returning to build of vcftools-0.1.17 ===> vcftools-0.1.17 depends on package: pkgconf>=1.3.0_1 - not found ===> Installing existing package /packages/All/pkgconf-3.0.5,1.pkg [144arm64-default-job-03] Installing pkgconf-3.0.5,1... [144arm64-default-job-03] Extracting pkgconf-3.0.5,1: .......... done ===> vcftools-0.1.17 depends on package: pkgconf>=1.3.0_1 - found ===> Returning to build of vcftools-0.1.17 ===> vcftools-0.1.17 depends on package: autoconf>=2.73 - not found ===> Installing existing package /packages/All/autoconf-2.73.pkg [144arm64-default-job-03] Installing autoconf-2.73... [144arm64-default-job-03] `-- Installing autoconf-switch-20220527... [144arm64-default-job-03] `-- Extracting autoconf-switch-20220527: .......... done [144arm64-default-job-03] `-- Installing m4-1.4.21,1... [144arm64-default-job-03] `-- Extracting m4-1.4.21,1: .......... done [144arm64-default-job-03] `-- Installing perl5-5.42.3... [144arm64-default-job-03] `-- Extracting perl5-5.42.3: .......... done [144arm64-default-job-03] Extracting autoconf-2.73: .......... done ===> vcftools-0.1.17 depends on package: autoconf>=2.73 - found ===> Returning to build of vcftools-0.1.17 ===> vcftools-0.1.17 depends on package: automake>=1.18.1 - not found ===> Installing existing package /packages/All/automake-1.18.1.pkg [144arm64-default-job-03] Installing automake-1.18.1... [144arm64-default-job-03] Extracting automake-1.18.1: .......... done ===> vcftools-0.1.17 depends on package: automake>=1.18.1 - found ===> Returning to build of vcftools-0.1.17 ===> vcftools-0.1.17 depends on package: perl5>=5.42.r<5.43 - found =========================================================================== =======================<phase: lib-depends >============================ ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =======================<phase: configure >============================ ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Configuring for vcftools-0.1.17 configure.ac:16: installing './compile' configure.ac:12: installing './install-sh' configure.ac:12: installing './missing' src/cpp/Makefile.am: installing './depcomp' configure: loading site script /usr/ports/Templates/config.site checking for a BSD-compatible install... /usr/bin/install -c checking whether sleep supports fractional seconds... yes checking filesystem timestamp resolution... 0.01 checking whether build environment is sane... yes checking for a race-free mkdir -p... (cached) /bin/mkdir -p checking for gawk... (cached) /usr/bin/awk checking whether /usr/local/bin/gmake sets $(MAKE)... yes checking whether /usr/local/bin/gmake supports nested variables... yes checking xargs -n works... yes checking whether UID '0' is supported by ustar format... yes checking whether GID '0' is supported by ustar format... yes checking how to create a ustar tar archive... (cached) /usr/bin/tar checking whether the C++ compiler works... yes checking for C++ compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C++... yes checking whether c++ accepts -g... yes checking whether /usr/local/bin/gmake supports the include directive... yes (GNU style) checking dependency style of c++... gcc3 checking for gcc... cc checking whether the compiler supports GNU C... yes checking whether cc accepts -g... yes checking for cc option to enable C23 features... unsupported checking for cc option to enable C11 features... none needed checking whether cc understands -c and -o together... yes checking dependency style of cc... gcc3 checking how to run the C preprocessor... cpp checking for perl... (cached) /usr/local/bin/perl checking pkg-config is at least version 0.9.0... ld-elf.so.1: Shared object "libpkgconf.so.8" not found, required by "pkgconf" no checking for zlib... no configure: error: in '/wrkdirs/usr/ports/biology/vcftools/work/vcftools-0.1.17': configure: error: A pkg-config implementation could not be found or is too old. Make sure it is in your PATH or set the PKG_CONFIG environment variable to the full path to pkg-config. Alternatively, you may set the environment variables ZLIB_CFLAGS and ZLIB_LIBS to avoid the need to call pkg-config. See the pkg-config man page for more details. To get a pkg-config implementation, see <http://github.com/pkgconf/pkgconf>. See 'config.log' for more details ===> Script "configure" failed unexpectedly. Please report the problem to [email protected] [maintainer] and attach the "/wrkdirs/usr/ports/biology/vcftools/work/vcftools-0.1.17/config.log" including the output of the failure of your make command. Also, it might be a good idea to provide an overview of all packages installed on your system (e.g. a /usr/local/sbin/pkg-static info -g -Ea). *** Error code 1 Stop. make: stopped making "configure" in /usr/ports/biology/vcftools
