From nobody Mon Feb 19 23:38:55 2024 X-Original-To: pkg-fallout@mlmmj.nyi.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2610:1c1:1:606c::19:1]) by mlmmj.nyi.freebsd.org (Postfix) with ESMTP id 4TdzWh3HXQz59l9p for ; Mon, 19 Feb 2024 23:38:56 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: from mxrelay.nyi.freebsd.org (mxrelay.nyi.freebsd.org [IPv6:2610:1c1:1:606c::19:3]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (4096 bits) server-digest SHA256 client-signature RSA-PSS (4096 bits) client-digest SHA256) (Client CN "mxrelay.nyi.freebsd.org", Issuer "R3" (verified OK)) by mx1.freebsd.org (Postfix) with ESMTPS id 4TdzWg49xkz4glT for ; Mon, 19 Feb 2024 23:38:55 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1708385935; h=from:from:reply-to:subject:subject:date:date:message-id:message-id: to:to:cc; bh=JwKcSffMPPl5bqP0Nfa3uWY5nx7Nm3dvfTnwxRbR20M=; b=WNiPibcn64w+BIFys1EVHc+dmH7Xb0PHjdVV5zADM3uE8U5fpfgANtrpAyE0UEcQk5yoqc aBzGyDoZAsHK29hNqnWOZod27T1EOmr+V6T10vhD3bsWKlkRVxCMVn3KHO82zzk7RtBYmb po6dSP36zaKjsVc3PbdJ5m3TU8Y8wypQ96MdYDiSLoflQ8vH/4cvhtmigZsXMj+gjrl5g2 xE7l2ZydCserC/WtgKHVEejHsTKrqmQRpJ6LbISs7URj30rSgrMnnTYGaZ093uKu2v8WS5 a1onBTC4agkU102xNZBrudYqOBBZyh5mwiz6APW6AoiwG9jaqVsjZpqBpHlXNQ== ARC-Authentication-Results: i=1; mx1.freebsd.org; none ARC-Seal: i=1; s=dkim; d=freebsd.org; t=1708385935; a=rsa-sha256; cv=none; b=ICtv4DT+Butwmq0bc0kAH3gXXGGuqdm6Ik/a/ck8d9ngh2gtqcvhIP0AONLhe6TJJe1qG1 IRhNmAZEz58kvaZHEW9WEFLmsPGHGqdoJT9lEEJbn/EKprRSibA7iboBFOGqhQT2KItAW5 XPecPwOcHDVudwBRnyJ72RItmV/sq1dCz0NNjEql2Vj6/fes58mn8NjdrSPEC1DRf7Xwq/ QKUYo1J5Ts8L9F52lRZdphiKNMzAdp678hG9iUI97a6fP1DsFD+p4KQv21DvxVpFqPgZTz oNso2ucL7u6JFJxl+lhMXQp0bmC2mAewdHKvzdr7M7mnuhg+/IiOaxZXbxJZHQ== Received: from foul1.nyi.freebsd.org (foul1.nyi.freebsd.org [IPv6:2610:1c1:1:6080::16:25]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (4096 bits) server-digest SHA256) (Client did not present a certificate) by mxrelay.nyi.freebsd.org (Postfix) with ESMTPS id 4TdzWg3FR5zvY2 for ; Mon, 19 Feb 2024 23:38:55 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: from foul1.nyi.freebsd.org (localhost [127.0.0.1]) by foul1.nyi.freebsd.org (8.17.1/8.17.1) with ESMTP id 41JNctt6087464 for ; Mon, 19 Feb 2024 23:38:55 GMT (envelope-from pkg-fallout@FreeBSD.org) Received: (from root@localhost) by foul1.nyi.freebsd.org (8.17.1/8.17.1/Submit) id 41JNctT9087463; Mon, 19 Feb 2024 23:38:55 GMT (envelope-from pkg-fallout@FreeBSD.org) Date: Mon, 19 Feb 2024 23:38:55 GMT From: pkg-fallout@FreeBSD.org Message-Id: <202402192338.41JNctT9087463@foul1.nyi.freebsd.org> To: pkg-fallout@FreeBSD.org Subject: [package - 140releng-powerpc-quarterly][biology/vcflib] Failed for vcflib-1.0.7 in build List-Id: Fallout logs from package building List-Archive: https://lists.freebsd.org/archives/freebsd-pkg-fallout List-Help: List-Post: List-Subscribe: List-Unsubscribe: Sender: owner-freebsd-pkg-fallout@freebsd.org 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/foul1/data/140releng-powerpc-quarterly/aa3532662c1f/logs/vcflib-1.0.7.log Build URL: https://pkg-status.freebsd.org/foul1/build.html?mastername=140releng-powerpc-quarterly&build=aa3532662c1f Log: =>> Building biology/vcflib build started at Mon Feb 19 23:38:09 UTC 2024 port directory: /usr/ports/biology/vcflib package name: vcflib-1.0.7 building for: FreeBSD 140releng-powerpc-quarterly-job-05 14.0-RELEASE-p4 FreeBSD 14.0-RELEASE-p4 1400097 powerpc maintained by: jwb@FreeBSD.org Makefile datestamp: -rw-r--r-- 1 root wheel 1806 Feb 3 01:03 /usr/ports/biology/vcflib/Makefile Ports top last git commit: aa3532662 Ports top unclean checkout: no Port dir last git commit: aa3532662 Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.1 Host OSVERSION: 1500003 Jail OSVERSION: 1400097 Job Id: 05 ---Begin Environment--- SHELL=/bin/sh BLOCKSIZE=K MAIL=/var/mail/root MM_CHARSET=UTF-8 LANG=C.UTF-8 OSVERSION=1400097 STATUS=1 HOME=/root PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin MAKE_OBJDIR_CHECK_WRITABLE=0 UNAME_m=powerpc UNAME_p=powerpc UNAME_r=14.0-RELEASE-p4 LOCALBASE=/usr/local UNAME_v=FreeBSD 14.0-RELEASE-p4 1400097 USER=root POUDRIERE_NAME=poudriere-git LIBEXECPREFIX=/usr/local/libexec/poudriere POUDRIERE_VERSION=3.4.1 MASTERMNT=/usr/local/poudriere/data/.m/140releng-powerpc-quarterly/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/140releng-powerpc-quarterly/05/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS MASTERNAME=140releng-powerpc-quarterly SCRIPTPREFIX=/usr/local/share/poudriere SCRIPTNAME=bulk.sh OLDPWD=/usr/local/poudriere/data/.m/140releng-powerpc-quarterly/ref/.p/pool POUDRIERE_PKGNAME=poudriere-git-3.4.1 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 vcflib-1.0.7: ZIG=off: Include Zig language support ===> Use 'make config' to modify these settings ---End OPTIONS List--- --MAINTAINER-- jwb@FreeBSD.org --End MAINTAINER-- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- MAKE=gmake PKG_CONFIG=pkgconf PYTHON="/usr/local/bin/python3.9" XDG_DATA_HOME=/wrkdirs/usr/ports/biology/vcflib/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/vcflib/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/vcflib/work/.cache HOME=/wrkdirs/usr/ports/biology/vcflib/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/vcflib/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/vcflib/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-- XDG_DATA_HOME=/wrkdirs/usr/ports/biology/vcflib/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/vcflib/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/vcflib/work/.cache HOME=/wrkdirs/usr/ports/biology/vcflib/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/vcflib/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/vcflib/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=" -fstack-protector-strong -L/usr/local/lib " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include " 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-- ZIG="@comment " NO_ZIG="" CMAKE_BUILD_TYPE="release" PYTHON_INCLUDEDIR=include/python3.9 PYTHON_LIBDIR=lib/python3.9 PYTHON_PLATFORM=freebsd14 PYTHON_SITELIBDIR=lib/python3.9/site-packages PYTHON_SUFFIX=39 PYTHON_EXT_SUFFIX=.cpython-39 PYTHON_VER=3.9 PYTHON_VERSION=python3.9 PYTHON2="@comment " PYTHON3="" OSREL=14.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/vcflib" EXAMPLESDIR="share/examples/vcflib" DATADIR="share/vcflib" WWWDIR="www/vcflib" ETCDIR="etc/vcflib" --End PLIST_SUB-- --SUB_LIST-- ZIG="@comment " NO_ZIG="" PYTHON_INCLUDEDIR=/usr/local/include/python3.9 PYTHON_LIBDIR=/usr/local/lib/python3.9 PYTHON_PLATFORM=freebsd14 PYTHON_SITELIBDIR=/usr/local/lib/python3.9/site-packages PYTHON_SUFFIX=39 PYTHON_EXT_SUFFIX=.cpython-39 PYTHON_VER=3.9 PYTHON_VERSION=python3.9 PYTHON2="@comment " PYTHON3="" PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/vcflib DOCSDIR=/usr/local/share/doc/vcflib EXAMPLESDIR=/usr/local/share/examples/vcflib WWWDIR=/usr/local/www/vcflib ETCDIR=/usr/local/etc/vcflib --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 MACHINE=powerpc MACHINE_ARCH=powerpc ARCH=${MACHINE_ARCH} #### #### # 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) 65536 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 --End resource limits-- =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> License MIT accepted by the user =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> vcflib-1.0.7 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.20.9.pkg [140releng-powerpc-quarterly-job-05] Installing pkg-1.20.9... [140releng-powerpc-quarterly-job-05] Extracting pkg-1.20.9: .......... done ===> vcflib-1.0.7 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of vcflib-1.0.7 =========================================================================== =================================================== ===== 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 vcflib-1.0.7 for building =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> License MIT accepted by the user ===> Fetching all distfiles required by vcflib-1.0.7 for building => SHA256 Checksum OK for ekg-vcflib-v1.0.7_GH0.tar.gz. => SHA256 Checksum OK for ekg-fastahack-bb33265_GH0.tar.gz. => SHA256 Checksum OK for ekg-filevercmp-df20dcc_GH0.tar.gz. => SHA256 Checksum OK for ekg-fsom-56695e1_GH0.tar.gz. => SHA256 Checksum OK for ekg-intervaltree-aa59377_GH0.tar.gz. => SHA256 Checksum OK for edawson-libVCFH-44b6580_GH0.tar.gz. => SHA256 Checksum OK for ekg-multichoose-e1f94ae_GH0.tar.gz. => SHA256 Checksum OK for ekg-smithwaterman-2610e25_GH0.tar.gz. => SHA256 Checksum OK for simd-everywhere-simde-no-tests-9af03cd_GH0.tar.gz. => SHA256 Checksum OK for vcflib-tabixpp-v1.1.2_GH0.tar.gz. =========================================================================== =================================================== ===== 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 vcflib-1.0.7 for building ===> Extracting for vcflib-1.0.7 => SHA256 Checksum OK for ekg-vcflib-v1.0.7_GH0.tar.gz. => SHA256 Checksum OK for ekg-fastahack-bb33265_GH0.tar.gz. => SHA256 Checksum OK for ekg-filevercmp-df20dcc_GH0.tar.gz. => SHA256 Checksum OK for ekg-fsom-56695e1_GH0.tar.gz. => SHA256 Checksum OK for ekg-intervaltree-aa59377_GH0.tar.gz. => SHA256 Checksum OK for edawson-libVCFH-44b6580_GH0.tar.gz. => SHA256 Checksum OK for ekg-multichoose-e1f94ae_GH0.tar.gz. => SHA256 Checksum OK for ekg-smithwaterman-2610e25_GH0.tar.gz. => SHA256 Checksum OK for simd-everywhere-simde-no-tests-9af03cd_GH0.tar.gz. => SHA256 Checksum OK for vcflib-tabixpp-v1.1.2_GH0.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 vcflib-1.0.7 ===> Applying FreeBSD patches for vcflib-1.0.7 from /usr/ports/biology/vcflib/files =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 [140releng-powerpc-quarterly-job-05] `-- Installing expat-2.5.0... [140releng-powerpc-quarterly-job-05] `-- Extracting expat-2.5.0: .......... done [140releng-powerpc-quarterly-job-05] `-- Installing jsoncpp-1.9.5... [140releng-powerpc-quarterly-job-05] `-- Extracting jsoncpp-1.9.5: .......... done [140releng-powerpc-quarterly-job-05] `-- Installing libuv-1.47.0... [140releng-powerpc-quarterly-job-05] `-- Extracting libuv-1.47.0: .......... done [140releng-powerpc-quarterly-job-05] `-- Installing rhash-1.4.4... [140releng-powerpc-quarterly-job-05] | `-- Installing gettext-runtime-0.22.3... [140releng-powerpc-quarterly-job-05] | | `-- Installing indexinfo-0.3.1... [140releng-powerpc-quarterly-job-05] | | `-- Extracting indexinfo-0.3.1: .... done [140releng-powerpc-quarterly-job-05] | `-- Extracting gettext-runtime-0.22.3: .......... done [140releng-powerpc-quarterly-job-05] `-- Extracting rhash-1.4.4: .......... done [140releng-powerpc-quarterly-job-05] Extracting cmake-core-3.28.1: .......... done ===> vcflib-1.0.7 depends on file: /usr/local/bin/cmake - found ===> Returning to build of vcflib-1.0.7 ===> vcflib-1.0.7 depends on package: gmake>=4.3 - not found ===> Installing existing package /packages/All/gmake-4.3_2.pkg [140releng-powerpc-quarterly-job-05] Installing gmake-4.3_2... [140releng-powerpc-quarterly-job-05] Extracting gmake-4.3_2: .......... done ===> vcflib-1.0.7 depends on package: gmake>=4.3 - found ===> Returning to build of vcflib-1.0.7 ===> vcflib-1.0.7 depends on package: pkgconf>=1.3.0_1 - not found ===> Installing existing package /packages/All/pkgconf-2.0.3_1,1.pkg [140releng-powerpc-quarterly-job-05] Installing pkgconf-2.0.3_1,1... [140releng-powerpc-quarterly-job-05] Extracting pkgconf-2.0.3_1,1: .......... done ===> vcflib-1.0.7 depends on package: pkgconf>=1.3.0_1 - found ===> Returning to build of vcflib-1.0.7 ===> vcflib-1.0.7 depends on file: /usr/local/bin/python3.9 - not found ===> Installing existing package /packages/All/python39-3.9.18.pkg [140releng-powerpc-quarterly-job-05] Installing python39-3.9.18... [140releng-powerpc-quarterly-job-05] `-- Installing libffi-3.4.4... [140releng-powerpc-quarterly-job-05] `-- Extracting libffi-3.4.4: .......... done [140releng-powerpc-quarterly-job-05] `-- Installing mpdecimal-2.5.1... [140releng-powerpc-quarterly-job-05] `-- Extracting mpdecimal-2.5.1: .......... done [140releng-powerpc-quarterly-job-05] `-- Installing readline-8.2.7... [140releng-powerpc-quarterly-job-05] `-- Extracting readline-8.2.7: .......... done [140releng-powerpc-quarterly-job-05] Extracting python39-3.9.18: .......... done ===== Message from python39-3.9.18: -- Note that some standard Python modules are provided as separate ports as they require additional dependencies. They are available as: py39-gdbm databases/py-gdbm@py39 py39-sqlite3 databases/py-sqlite3@py39 py39-tkinter x11-toolkits/py-tkinter@py39 ===> vcflib-1.0.7 depends on file: /usr/local/bin/python3.9 - found ===> Returning to build of vcflib-1.0.7 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> vcflib-1.0.7 depends on shared library: libhts.so - not found ===> Installing existing package /packages/All/htslib-1.17.pkg [140releng-powerpc-quarterly-job-05] Installing htslib-1.17... [140releng-powerpc-quarterly-job-05] `-- Installing curl-8.5.0... [140releng-powerpc-quarterly-job-05] | `-- Installing libnghttp2-1.58.0... [140releng-powerpc-quarterly-job-05] | `-- Extracting libnghttp2-1.58.0: .......... done [140releng-powerpc-quarterly-job-05] | `-- Installing libpsl-0.21.2_4... [140releng-powerpc-quarterly-job-05] | | `-- Installing libidn2-2.3.4... [140releng-powerpc-quarterly-job-05] | | `-- Installing libunistring-1.1... [140releng-powerpc-quarterly-job-05] | | `-- Extracting libunistring-1.1: .......... done [140releng-powerpc-quarterly-job-05] | | `-- Extracting libidn2-2.3.4: .......... done [140releng-powerpc-quarterly-job-05] | `-- Extracting libpsl-0.21.2_4: .......... done [140releng-powerpc-quarterly-job-05] | `-- Installing libssh2-1.11.0,3... [140releng-powerpc-quarterly-job-05] | `-- Extracting libssh2-1.11.0,3: .......... done [140releng-powerpc-quarterly-job-05] `-- Extracting curl-8.5.0: .......... done [140releng-powerpc-quarterly-job-05] `-- Installing libdeflate-1.19... [140releng-powerpc-quarterly-job-05] `-- Extracting libdeflate-1.19: .......... done [140releng-powerpc-quarterly-job-05] Extracting htslib-1.17: .......... done ===> vcflib-1.0.7 depends on shared library: libhts.so - found (/usr/local/lib/libhts.so) ===> Returning to build of vcflib-1.0.7 ===> vcflib-1.0.7 depends on shared library: libcurl.so - found (/usr/local/lib/libcurl.so) ===> vcflib-1.0.7 depends on shared library: libwfa2.so - not found ===> Installing existing package /packages/All/wfa2-lib-2.3.4.pkg [140releng-powerpc-quarterly-job-05] Installing wfa2-lib-2.3.4... [140releng-powerpc-quarterly-job-05] Extracting wfa2-lib-2.3.4: .......... done ===> vcflib-1.0.7 depends on shared library: libwfa2.so - found (/usr/local/lib/libwfa2.so) ===> Returning to build of vcflib-1.0.7 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Configuring for vcflib-1.0.7 ===> Performing out-of-source build /bin/mkdir -p /wrkdirs/usr/ports/biology/vcflib/work/.build -- The C compiler identification is Clang 16.0.6 -- The CXX compiler identification is Clang 16.0.6 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Found PkgConfig: /usr/local/bin/pkgconf (found version "2.0.3") CMake Warning (dev) at /usr/local/share/cmake/pybind11/FindPythonLibsNew.cmake:98 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): /usr/local/share/cmake/pybind11/pybind11Tools.cmake:50 (find_package) /usr/local/share/cmake/pybind11/pybind11Common.cmake:188 (include) /usr/local/share/cmake/pybind11/pybind11Config.cmake:250 (include) CMakeLists.txt:19 (find_package) This warning is for project developers. Use -Wno-dev to suppress it. -- Found PythonInterp: /usr/local/bin/python3.9 (found suitable version "3.9.18", minimum required is "3.6") -- Found PythonLibs: /usr/local/lib/libpython3.9.so -- Performing Test HAS_FLTO -- Performing Test HAS_FLTO - Success -- Performing Test HAS_FLTO_THIN -- Performing Test HAS_FLTO_THIN - Success -- Found pybind11: /usr/local/include (found version "2.11.1") -- Found BZip2: /usr/lib/libbz2.so (found version "1.0.8") -- Looking for BZ2_bzCompressInit -- Looking for BZ2_bzCompressInit - found -- Looking for lzma_auto_decoder in /usr/lib/liblzma.so -- Looking for lzma_auto_decoder in /usr/lib/liblzma.so - found -- Looking for lzma_easy_encoder in /usr/lib/liblzma.so -- Looking for lzma_easy_encoder in /usr/lib/liblzma.so - found -- Looking for lzma_lzma_preset in /usr/lib/liblzma.so -- Looking for lzma_lzma_preset in /usr/lib/liblzma.so - found -- Found LibLZMA: /usr/lib/liblzma.so (found version "5.4.4") -- Found ZLIB: /usr/lib/libz.so (found version "1.3") -- Found CURL: /usr/local/lib/libcurl.so (found version "8.5.0") -- -- Could NOT find OpenMP_C (missing: OpenMP_C_FLAGS OpenMP_C_LIB_NAMES) -- Could NOT find OpenMP_CXX (missing: OpenMP_CXX_FLAGS OpenMP_CXX_LIB_NAMES) -- Could NOT find OpenMP (missing: OpenMP_C_FOUND OpenMP_CXX_FOUND) -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Failed -- Looking for pthread_create in pthreads -- Looking for pthread_create in pthreads - not found -- Looking for pthread_create in pthread -- Looking for pthread_create in pthread - not found -- Found Threads: TRUE -- Checking for module 'htslib' -- Found htslib, version 1.17 -- Checking for module 'tabixpp' -- Package 'tabixpp', required by 'virtual:world', not found -- WFA using include /usr/local/include/wfa2lib Pandoc needs to be installed to generate the man pages -- Configuring done (24.3s) -- Generating done (1.7s) CMake Warning: Manually-specified variables were not used by the project: BOOST_PYTHON_SUFFIX CMAKE_SHARED_LINKER_FLAGS FETCHCONTENT_FULLY_DISCONNECTED Python3_EXECUTABLE Python_EXECUTABLE -- Build files have been written to: /wrkdirs/usr/ports/biology/vcflib/work/.build =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building for vcflib-1.0.7 gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/vcflib/work/.build' /usr/local/bin/cmake -S/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7 -B/wrkdirs/usr/ports/biology/vcflib/work/.build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/local/bin/cmake -E cmake_progress_start /wrkdirs/usr/ports/biology/vcflib/work/.build/CMakeFiles /wrkdirs/usr/ports/biology/vcflib/work/.build//CMakeFiles/progress.marks gmake -f CMakeFiles/Makefile2 all gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/vcflib/work/.build' gmake -f CMakeFiles/vcflib.dir/build.make CMakeFiles/vcflib.dir/depend gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/vcflib/work/.build' cd /wrkdirs/usr/ports/biology/vcflib/work/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7 /wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7 /wrkdirs/usr/ports/biology/vcflib/work/.build /wrkdirs/usr/ports/biology/vcflib/work/.build /wrkdirs/usr/ports/biology/vcflib/work/.build/CMakeFiles/vcflib.dir/DependInfo.cmake gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/vcflib/work/.build' gmake -f CMakeFiles/vcflib.dir/build.make CMakeFiles/vcflib.dir/build gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/vcflib/work/.build' [ 1%] Building CXX object CMakeFiles/vcflib.dir/src/legacy.cpp.o [ 1%] Building CXX object CMakeFiles/vcflib.dir/src/vcf-c-api.cpp.o /usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/include -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/contrib/fastahack -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/contrib/intervaltree -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/contrib/smithwaterman -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/contrib/multichoose -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/contrib/filevercmp -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/contrib/c-progress-bar -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/contrib/tabixpp -I/usr/local/include/wfa2lib NOTFOUND -D_FILE_OFFSET_BITS=64 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=gnu++14 -flto=thin -fPIC -MD -MT CMakeFiles/vcflib.dir/src/legacy.cpp.o -MF CMakeFiles/vcflib.dir/src/legacy.cpp.o.d -o CMakeFiles/vcflib.dir/src/legacy.cpp.o -c /wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/src/legacy.cpp [ 1%] Building CXX object CMakeFiles/vcflib.dir/src/Variant.cpp.o /usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/include -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/contrib/fastahack -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/contrib/intervaltree -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/contrib/smithwaterman -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/contrib/multichoose -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/contrib/filevercmp -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/contrib/c-progress-bar -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/contrib/tabixpp -I/usr/local/include/wfa2lib NOTFOUND -D_FILE_OFFSET_BITS=64 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=gnu++14 -flto=thin -fPIC -MD -MT CMakeFiles/vcflib.dir/src/Variant.cpp.o -MF CMakeFiles/vcflib.dir/src/Variant.cpp.o.d -o CMakeFiles/vcflib.dir/src/Variant.cpp .o -c /wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/src/Variant.cpp /usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/include -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/contrib/fastahack -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/contrib/intervaltree -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/contrib/smithwaterman -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/contrib/multichoose -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/contrib/filevercmp -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/contrib/c-progress-bar -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/contrib/tabixpp -I/usr/local/include/wfa2lib NOTFOUND -D_FILE_OFFSET_BITS=64 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=gnu++14 -flto=thin -fPIC -MD -MT CMakeFiles/vcflib.dir/src/vcf-c-api.cpp.o -MF CMakeFiles/vcflib.dir/src/vcf-c-api.cpp.o.d -o CMakeFiles/vcflib.dir/src/vcf-c-a pi.cpp.o -c /wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/src/vcf-c-api.cpp c++: error: no such file or directory: 'NOTFOUND' gmake[3]: *** [CMakeFiles/vcflib.dir/build.make:93: CMakeFiles/vcflib.dir/src/legacy.cpp.o] Error 1 gmake[3]: *** Waiting for unfinished jobs.... c++: error: no such file or directory: 'NOTFOUND' gmake[3]: *** [CMakeFiles/vcflib.dir/build.make:79: CMakeFiles/vcflib.dir/src/vcf-c-api.cpp.o] Error 1 c++: error: no such file or directory: 'NOTFOUND' gmake[3]: *** [CMakeFiles/vcflib.dir/build.make:107: CMakeFiles/vcflib.dir/src/Variant.cpp.o] Error 1 gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/vcflib/work/.build' gmake[2]: *** [CMakeFiles/Makefile2:258: CMakeFiles/vcflib.dir/all] Error 2 gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/vcflib/work/.build' gmake[1]: *** [Makefile:149: all] Error 2 gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/vcflib/work/.build' ===> 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 in /usr/ports/biology/vcflib