From nobody Fri Jun 30 03:56:43 2023 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 4QshMc0kgRz4lDnf for ; Fri, 30 Jun 2023 03:56:44 +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 4QshMb5lp1z3NgY for ; Fri, 30 Jun 2023 03:56:43 +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=1688097403; h=from:from:reply-to:subject:subject:date:date:message-id:message-id: to:to:cc; bh=+ZhAn31OQciriwk+qjVWX81j5KkQNTSs+AANa/Ctdjs=; b=HE6fGQxBuVy+QAkcyG98copsZ7DC1B8VxA5HUQgcXUHmgKOuwMkq8ddxzuSeIgmwr14PFC U1z9Avs8f9oQeiu6/rFGztlgiDdxvxyMOBw8uvhcfThRcy4JXjPTZXUdV9M/kw3c1/pSM6 hw7hXB1sQL8bKQ0YnIwHYTSsYr2wf4O0t8elXQ9mVtDSp0kkPOWmQX1x8ReDoCkUu7RJef Z/FazSrFKa2Xrn4Hnp05N2ivcuNUBbriUtpFEDn/JhAfklFVPgRodeOAVu+47kmS8YxIPd D1vpga50jPoO7ETNOoNs7VLIVzTwDvVI6JE9CAtdKSwIhDGTSsl9Yl5J7tEyeQ== ARC-Authentication-Results: i=1; mx1.freebsd.org; none ARC-Seal: i=1; s=dkim; d=freebsd.org; t=1688097403; a=rsa-sha256; cv=none; b=eUBN3eY3FOJDHkGuPd3UNqlluxD16RHC9FS56srhHWg7QV12xpyPBfCSVE71rRPhBTYYlk 6mQMgYy/xrtt68ZtBADW9qPS4jMmyt0jjLlGD38I3fokafzZKGqRH6IHQ+3KfUnF8dIt5F Kbc4Xx8jIxKtFja0z0e5a1HuyunBtu/I53zY1qYuRFuA5GZkYbwNJd+WBimemlv4Zn8RJw 3cKEA0u/v4lO+MfeMJ/QLkNfy+1paV2vH+AzqhysoN6idLt10PzGiDKNvoEl7eUV/YR+bX gncW00v24JhibIkrT4mg67BpOvuaB08xn52gN1fBsC5HaCvHvXTlwlWt+dpMYA== Received: from ampere3.nyi.freebsd.org (ampere3.nyi.freebsd.org [IPv6:2610:1c1:1:6080::16:26]) by mxrelay.nyi.freebsd.org (Postfix) with ESMTP id 4QshMb4pPFzkgQ for ; Fri, 30 Jun 2023 03:56:43 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: from root (uid 0) (envelope-from pkg-fallout@FreeBSD.org) id 20e1 by ampere3.nyi.freebsd.org (DragonFly Mail Agent v0.13+ on ampere3.nyi.freebsd.org); Fri, 30 Jun 2023 03:56:43 +0000 To: pkg-fallout@FreeBSD.org Subject: [package - 131releng-armv7-default][biology/vcflib] Failed for vcflib-1.0.7 in build Date: Fri, 30 Jun 2023 03:56:43 +0000 Message-Id: <649e527b.20e1.5cd125c6@ampere3.nyi.freebsd.org> From: X-ThisMailContainsUnwantedMimeParts: N 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/ampere3/data/131releng-armv7-default/4785b313b958/logs/vcflib-1.0.7.log Build URL: https://pkg-status.freebsd.org/ampere3/build.html?mastername=131releng-armv7-default&build=4785b313b958 Log: =>> Building biology/vcflib build started at Fri Jun 30 03:56:25 UTC 2023 port directory: /usr/ports/biology/vcflib package name: vcflib-1.0.7 building for: FreeBSD 131releng-armv7-default-job-02 13.1-RELEASE-p8 FreeBSD 13.1-RELEASE-p8 1301000 arm maintained by: jwb@FreeBSD.org Makefile ident: Poudriere version: 3.2.8-23-ga7f8d188 Host OSVERSION: 1400089 Jail OSVERSION: 1301000 Job Id: 02 ---Begin Environment--- SHELL=/bin/csh OSVERSION=1301000 UNAME_v=FreeBSD 13.1-RELEASE-p8 1301000 UNAME_r=13.1-RELEASE-p8 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 LIBEXECPREFIX=/usr/local/libexec/poudriere POUDRIERE_VERSION=3.2.8-23-ga7f8d188 MASTERMNT=/usr/local/poudriere/data/.m/131releng-armv7-default/ref POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM= PWD=/usr/local/poudriere/data/.m/131releng-armv7-default/ref/.p/pool P_PORTS_FEATURES=FLAVORS SELECTED_OPTIONS MASTERNAME=131releng-armv7-default SCRIPTPREFIX=/usr/local/share/poudriere OLDPWD=/usr/local/poudriere/data/.m/131releng-armv7-default/ref/.p SCRIPTPATH=/usr/local/share/poudriere/bulk.sh POUDRIEREPATH=/usr/local/bin/poudriere ---End Environment--- ---Begin Poudriere Port Flags/Env--- PORT_FLAGS= PKGENV= FLAVOR= DEPENDS_ARGS= 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_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-- ZIG="@comment " NO_ZIG="" CMAKE_BUILD_TYPE="release" PYTHON_INCLUDEDIR=include/python3.9 PYTHON_LIBDIR=lib/python3.9 PYTHON_PLATFORM=freebsd13 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=13.1 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=freebsd13 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 #### /usr/local/etc/poudriere.d/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 2 jobs MAKE_JOBS_NUMBER=2 #### /usr/ports/Mk/Scripts/ports_env.sh #### _CCVERSION_921dbbb2=FreeBSD clang version 13.0.0 (git@github.com:llvm/llvm-project.git llvmorg-13.0.0-0-gd7b669b3a303) Target: armv7-unknown-freebsd13.1-gnueabihf Thread model: posix InstalledDir: /usr/bin _ALTCCVERSION_921dbbb2=none _CXXINTERNAL_acaad9ca=FreeBSD clang version 13.0.0 (git@github.com:llvm/llvm-project.git llvmorg-13.0.0-0-gd7b669b3a303) Target: armv7-unknown-freebsd13.1-gnueabihf Thread model: posix InstalledDir: /usr/bin "/usr/bin/ld" "--eh-frame-hdr" "-dynamic-linker" "/libexec/ld-elf.so.1" "--hash-style=both" "--enable-new-dtags" "-o" "a.out" "/usr/lib/crt1.o" "/usr/lib/crti.o" "/usr/lib/crtbegin.o" "-L/usr/lib" "/dev/null" "-lc++" "-lm" "-lgcc" "--as-needed" "-lgcc_s" "--no-as-needed" "-lc" "-lgcc" "--as-needed" "-lgcc_s" "--no-as-needed" "/usr/lib/crtend.o" "/usr/lib/crtn.o" CC_OUTPUT_921dbbb2_58173849=yes CC_OUTPUT_921dbbb2_9bdba57c=yes CC_OUTPUT_921dbbb2_6a4fe7f5=yes CC_OUTPUT_921dbbb2_6bcac02b=yes CC_OUTPUT_921dbbb2_67d20829=yes CC_OUTPUT_921dbbb2_bfa62e83=yes CC_OUTPUT_921dbbb2_f0b4d593=yes CC_OUTPUT_921dbbb2_308abb44=yes CC_OUTPUT_921dbbb2_f00456e5=yes CC_OUTPUT_921dbbb2_65ad290d=yes CC_OUTPUT_921dbbb2_f2776b26=yes CC_OUTPUT_921dbbb2_53255a77=yes CC_OUTPUT_921dbbb2_911cfe02=yes CC_OUTPUT_921dbbb2_b2657cc3=yes CC_OUTPUT_921dbbb2_380987f7=yes CC_OUTPUT_921dbbb2_160933ec=yes CC_OUTPUT_921dbbb2_fb62803b=yes CC_OUTPUT_921dbbb2_af59ad06=yes CC_OUTPUT_921dbbb2_a15f3fcf=yes _OBJC_CCVERSION_921dbbb2=FreeBSD clang version 13.0.0 (git@github.com:llvm/llvm-project.git llvmorg-13.0.0-0-gd7b669b3a303) Target: armv7-unknown-freebsd13.1-gnueabihf Thread model: posix InstalledDir: /usr/bin _OBJC_ALTCCVERSION_921dbbb2=none ARCH=armv7 OPSYS=FreeBSD _OSRELEASE=13.1-RELEASE-p8 OSREL=13.1 OSVERSION=1301000 PYTHONBASE=/usr/local CONFIGURE_MAX_CMD_LEN=524288 HAVE_PORTS_ENV=1 #### Misc Poudriere #### 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) 1024 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-- =================================================== ===> License MIT accepted by the user =========================================================================== =================================================== ===> vcflib-1.0.7 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.19.1_1.pkg [131releng-armv7-default-job-02] Installing pkg-1.19.1_1... [131releng-armv7-default-job-02] Extracting pkg-1.19.1_1: .......... done ===> vcflib-1.0.7 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of vcflib-1.0.7 =========================================================================== =================================================== =========================================================================== =================================================== ===> License MIT accepted by the user ===> Fetching all distfiles required by vcflib-1.0.7 for building =========================================================================== =================================================== ===> 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. =========================================================================== =================================================== =========================================================================== =================================================== ===> 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. =========================================================================== =================================================== [131releng-armv7-default-job-02] `-- Extracting libuv-1.45.0: .......... done [131releng-armv7-default-job-02] `-- Installing rhash-1.4.3... [131releng-armv7-default-job-02] | `-- Installing gettext-runtime-0.21.1... [131releng-armv7-default-job-02] | | `-- Installing indexinfo-0.3.1... [131releng-armv7-default-job-02] | | `-- Extracting indexinfo-0.3.1: .... done [131releng-armv7-default-job-02] | `-- Extracting gettext-runtime-0.21.1: .......... done [131releng-armv7-default-job-02] `-- Extracting rhash-1.4.3: .......... done [131releng-armv7-default-job-02] Extracting cmake-core-3.26.1_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 [131releng-armv7-default-job-02] Installing gmake-4.3_2... [131releng-armv7-default-job-02] 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-1.8.1,1.pkg [131releng-armv7-default-job-02] Installing pkgconf-1.8.1,1... [131releng-armv7-default-job-02] Extracting pkgconf-1.8.1,1: .......... 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/python39-3.9.17.pkg [131releng-armv7-default-job-02] Installing python39-3.9.17... [131releng-armv7-default-job-02] `-- Installing libffi-3.4.4... [131releng-armv7-default-job-02] `-- Extracting libffi-3.4.4: .......... done [131releng-armv7-default-job-02] `-- Installing mpdecimal-2.5.1... [131releng-armv7-default-job-02] `-- Extracting mpdecimal-2.5.1: .......... done [131releng-armv7-default-job-02] `-- Installing readline-8.2.1... [131releng-armv7-default-job-02] `-- Extracting readline-8.2.1: .......... done [131releng-armv7-default-job-02] Extracting python39-3.9.17: .......... done ===== Message from python39-3.9.17: -- 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 =========================================================================== =================================================== ===> vcflib-1.0.7 depends on shared library: libhts.so - not found ===> Installing existing package /packages/All/htslib-1.17.pkg [131releng-armv7-default-job-02] Installing htslib-1.17... [131releng-armv7-default-job-02] `-- Installing curl-8.1.2... [131releng-armv7-default-job-02] | `-- Installing ca_root_nss-3.89.1... [131releng-armv7-default-job-02] | `-- Extracting ca_root_nss-3.89.1: .......... done [131releng-armv7-default-job-02] | `-- Installing libnghttp2-1.53.0... [131releng-armv7-default-job-02] | `-- Extracting libnghttp2-1.53.0: .......... done [131releng-armv7-default-job-02] | `-- Installing libpsl-0.21.2_3... [131releng-armv7-default-job-02] | | `-- Installing libidn2-2.3.4... [131releng-armv7-default-job-02] | | `-- Installing libunistring-1.1... [131releng-armv7-default-job-02] | | `-- Extracting libunistring-1.1: .......... done [131releng-armv7-default-job-02] | | `-- Extracting libidn2-2.3.4: .......... done [131releng-armv7-default-job-02] | `-- Extracting libpsl-0.21.2_3: .......... done [131releng-armv7-default-job-02] | `-- Installing libssh2-1.11.0,3... [131releng-armv7-default-job-02] | `-- Extracting libssh2-1.11.0,3: .......... done [131releng-armv7-default-job-02] `-- Extracting curl-8.1.2: .......... done [131releng-armv7-default-job-02] `-- Installing libdeflate-1.18... [131releng-armv7-default-job-02] `-- Extracting libdeflate-1.18: .......... done [131releng-armv7-default-job-02] Extracting htslib-1.17: .......... done ===== Message from ca_root_nss-3.89.1: -- FreeBSD does not, and can not warrant that the certification authorities whose certificates are included in this package have in any way been audited for trustworthiness or RFC 3647 compliance. Assessment and verification of trust is the complete responsibility of the system administrator. This package installs symlinks to support root certificates discovery by default for software that uses OpenSSL. This enables SSL Certificate Verification by client software without manual intervention. If you prefer to do this manually, replace the following symlinks with either an empty file or your site-local certificate bundle. * /etc/ssl/cert.pem * /usr/local/etc/ssl/cert.pem * /usr/local/openssl/cert.pem ===> 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-2.3.2_1.pkg [131releng-armv7-default-job-02] Installing wfa2-lib-2.3.2_1... [131releng-armv7-default-job-02] Extracting wfa2-lib-2.3.2_1: .......... 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 =========================================================================== =================================================== ===> 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 13.0.0 -- The CXX compiler identification is Clang 13.0.0 -- 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 "1.8.1") -- Found PythonInterp: /usr/local/bin/python3.9 (found suitable version "3.9.17", 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 "2.10.4") -- 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 "5.2.5") -- Found ZLIB: /usr/lib/libz.so (found version "1.2.12") -- Found CURL: /usr/local/lib/libcurl.so (found version "8.1.2") -- -- 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 (4.5s) -- Generating done (0.5s) CMake Warning: Manually-specified variables were not used by the project: BOOST_PYTHON_SUFFIX CMAKE_SHARED_LINKER_FLAGS FETCHCONTENT_FULLY_DISCONNECTED -- Build files have been written to: /wrkdirs/usr/ports/biology/vcflib/work/.build =========================================================================== =================================================== ===> 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/lega cy.cpp.o -c /wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/src/legacy.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/sr c/vcf-c-api.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 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