[exp - 123amd64-default-build-as-user][biology/vcflib] Failed for vcflib-1.0.5_1 in build
- Go to: [ bottom of page ] [ top of archives ] [ this month ]
Date: Fri, 27 Jan 2023 16:26:14 UTC
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/package19/data/123amd64-default-build-as-user/fe81050c2fda/logs/vcflib-1.0.5_1.log
Build URL: https://pkg-status.freebsd.org/package19/build.html?mastername=123amd64-default-build-as-user&build=fe81050c2fda
Log:
=>> Building biology/vcflib
build started at Fri Jan 27 16:24:59 UTC 2023
port directory: /usr/ports/biology/vcflib
package name: vcflib-1.0.5_1
building for: FreeBSD 123amd64-default-build-as-user-job-03 12.3-RELEASE-p10 FreeBSD 12.3-RELEASE-p10 amd64
maintained by: jwb@FreeBSD.org
Makefile ident:
Poudriere version: 3.2.8-23-ga7f8d188
Host OSVERSION: 1400073
Jail OSVERSION: 1203000
Job Id: 03
---Begin Environment---
SHELL=/bin/csh
OSVERSION=1203000
UNAME_v=FreeBSD 12.3-RELEASE-p10
UNAME_r=12.3-RELEASE-p10
BLOCKSIZE=K
MAIL=/var/mail/root
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=/poudriere/data/.m/123amd64-default-build-as-user/ref
POUDRIERE_BUILD_TYPE=bulk
PACKAGE_BUILDING=yes
SAVED_TERM=
GID=0
UID=0
PWD=/poudriere/data/.m/123amd64-default-build-as-user/ref/.p/pool
P_PORTS_FEATURES=FLAVORS SELECTED_OPTIONS
MASTERNAME=123amd64-default-build-as-user
SCRIPTPREFIX=/usr/local/share/poudriere
OLDPWD=/poudriere/data/.m/123amd64-default-build-as-user/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---
---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--
CMAKE_BUILD_TYPE="release" PYTHON_INCLUDEDIR=include/python3.9 PYTHON_LIBDIR=lib/python3.9 PYTHON_PLATFORM=freebsd12 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=12.3 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--
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
FORCE_PACKAGE=yes
PACKAGE_BUILDING=yes
PACKAGE_BUILDING_FLAVORS=yes
#### /usr/local/etc/poudriere.d/make.conf ####
# Build ALLOW_MAKE_JOBS_PACKAGES with 2 jobs
MAKE_JOBS_NUMBER=2
#### /usr/ports/Mk/Scripts/ports_env.sh ####
_CCVERSION_921dbbb2=FreeBSD clang version 10.0.1 (git@github.com:llvm/llvm-project.git llvmorg-10.0.1-0-gef32c611aa2) Target: x86_64-unknown-freebsd12.3 Thread model: posix InstalledDir: /usr/bin
_ALTCCVERSION_921dbbb2=none
_CXXINTERNAL_acaad9ca=FreeBSD clang version 10.0.1 (git@github.com:llvm/llvm-project.git llvmorg-10.0.1-0-gef32c611aa2) Target: x86_64-unknown-freebsd12.3 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=error: invalid value 'c++2b' in '-std=c++2b' note: use 'c++98' or 'c++03' for 'ISO C++ 1998 with amendments' standard note: use 'gnu++98' or 'gnu++03' for 'ISO C++ 1998 with amendments and GNU extensions' standard note: use 'c++11' for 'ISO C++ 2011 with amendments' standard note: use 'gnu++11' for 'ISO C++ 2011 with amendments and GNU extensions' standard note: use 'c++14' for 'ISO C++ 2014 with amendments' standard note: use 'gnu++14' for 'ISO C++ 2014 with amendments and GNU extensions' standard note: use 'c++17' for 'ISO C++ 2017 with amendments' standard note: use 'gnu++17' for 'ISO C++ 2017 with amendments and GNU extensions' standard note: use 'c++20' for 'ISO C++ 2020 DIS' standard note: use 'gnu++20' for 'ISO C++ 2020 DIS with GNU extensions' standard
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=error: invalid value 'gnu++2b' in '-std=gnu++2b' note: use 'c++98' or 'c++03' for 'ISO C++ 1998 with amendments' standard note: use 'gnu++98' or 'gnu++03' for 'ISO C++ 1998 with amendments and GNU extensions' standard note: use 'c++11' for 'ISO C++ 2011 with amendments' standard note: use 'gnu++11' for 'ISO C++ 2011 with amendments and GNU extensions' standard note: use 'c++14' for 'ISO C++ 2014 with amendments' standard note: use 'gnu++14' for 'ISO C++ 2014 with amendments and GNU extensions' standard note: use 'c++17' for 'ISO C++ 2017 with amendments' standard note: use 'gnu++17' for 'ISO C++ 2017 with amendments and GNU extensions' standard note: use 'c++20' for 'ISO C++ 2020 DIS' standard note: use 'gnu++20' for 'ISO C++ 2020 DIS with GNU extensions' standard
_OBJC_CCVERSION_921dbbb2=FreeBSD clang version 10.0.1 (git@github.com:llvm/llvm-project.git llvmorg-10.0.1-0-gef32c611aa2) Target: x86_64-unknown-freebsd12.3 Thread model: posix InstalledDir: /usr/bin
_OBJC_ALTCCVERSION_921dbbb2=none
ARCH=amd64
OPSYS=FreeBSD
_OSRELEASE=12.3-RELEASE-p10
OSREL=12.3
OSVERSION=1203000
PYTHONBASE=/usr/local
HAVE_COMPAT_IA32_KERN=YES
CONFIGURE_MAX_CMD_LEN=524288
HAVE_PORTS_ENV=1
#### Misc Poudriere ####
---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) 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--
=======================<phase: check-sanity >============================
===> License MIT accepted by the user
===========================================================================
=======================<phase: pkg-depends >============================
===> vcflib-1.0.5_1 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-1.19.0.pkg
[123amd64-default-build-as-user-job-03] Installing pkg-1.19.0...
[123amd64-default-build-as-user-job-03] Extracting pkg-1.19.0: .......... done
===> vcflib-1.0.5_1 depends on file: /usr/local/sbin/pkg - found
===> Returning to build of vcflib-1.0.5_1
===========================================================================
=======================<phase: fetch-depends >============================
===========================================================================
=======================<phase: fetch >============================
===> License MIT accepted by the user
=> ekg-vcflib-v1.0.5_GH0.tar.gz doesn't seem to exist in /portdistfiles/.
=> Attempting to fetch https://codeload.github.com/ekg/vcflib/tar.gz/v1.0.5?dummy=/ekg-vcflib-v1.0.5_GH0.tar.gz
fetch: https://codeload.github.com/ekg/vcflib/tar.gz/v1.0.5?dummy=/ekg-vcflib-v1.0.5_GH0.tar.gz: size unknown
fetch: https://codeload.github.com/ekg/vcflib/tar.gz/v1.0.5?dummy=/ekg-vcflib-v1.0.5_GH0.tar.gz: size of remote file is not known
ekg-vcflib-v1.0.5_GH0.tar.gz 22 MB 5374 kBps 04s
=> vcflib-tabixpp-v1.1.2_GH0.tar.gz doesn't seem to exist in /portdistfiles/.
=> Attempting to fetch https://codeload.github.com/vcflib/tabixpp/tar.gz/v1.1.2?dummy=/vcflib-tabixpp-v1.1.2_GH0.tar.gz
fetch: https://codeload.github.com/vcflib/tabixpp/tar.gz/v1.1.2?dummy=/vcflib-tabixpp-v1.1.2_GH0.tar.gz: size unknown
fetch: https://codeload.github.com/vcflib/tabixpp/tar.gz/v1.1.2?dummy=/vcflib-tabixpp-v1.1.2_GH0.tar.gz: size of remote file is not known
vcflib-tabixpp-v1.1.2_GH0.tar.gz 6962 B 675 kBps 00s
=> smarco-WFA2-lib-v2.3_GH0.tar.gz doesn't seem to exist in /portdistfiles/.
=> Attempting to fetch https://codeload.github.com/smarco/WFA2-lib/tar.gz/v2.3?dummy=/smarco-WFA2-lib-v2.3_GH0.tar.gz
fetch: https://codeload.github.com/smarco/WFA2-lib/tar.gz/v2.3?dummy=/smarco-WFA2-lib-v2.3_GH0.tar.gz: size unknown
fetch: https://codeload.github.com/smarco/WFA2-lib/tar.gz/v2.3?dummy=/smarco-WFA2-lib-v2.3_GH0.tar.gz: size of remote file is not known
smarco-WFA2-lib-v2.3_GH0.tar.gz 4051 kB 5719 kBps 00s
===> Fetching all distfiles required by vcflib-1.0.5_1 for building
===========================================================================
=======================<phase: checksum >============================
===> License MIT accepted by the user
===> Fetching all distfiles required by vcflib-1.0.5_1 for building
=> SHA256 Checksum OK for ekg-vcflib-v1.0.5_GH0.tar.gz.
=> SHA256 Checksum OK for ekg-fastahack-bb33265_GH0.tar.gz.
=> SHA256 Checksum OK for ekg-filevercmp-1a9b779_GH0.tar.gz.
=> SHA256 Checksum OK for ekg-fsom-a6ef318_GH0.tar.gz.
=> SHA256 Checksum OK for google-googletest-d225acc_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-68733cd_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.
=> SHA256 Checksum OK for smarco-WFA2-lib-v2.3_GH0.tar.gz.
===========================================================================
=======================<phase: extract-depends>============================
===========================================================================
=======================<phase: extract >============================
===> License MIT accepted by the user
===> Fetching all distfiles required by vcflib-1.0.5_1 for building
===> Extracting for vcflib-1.0.5_1
=> SHA256 Checksum OK for ekg-vcflib-v1.0.5_GH0.tar.gz.
=> SHA256 Checksum OK for ekg-fastahack-bb33265_GH0.tar.gz.
=> SHA256 Checksum OK for ekg-filevercmp-1a9b779_GH0.tar.gz.
<snip>
[123amd64-default-build-as-user-job-03] `-- Extracting curl-7.87.0_1: .......... done
[123amd64-default-build-as-user-job-03] `-- Installing libdeflate-1.17...
[123amd64-default-build-as-user-job-03] `-- Extracting libdeflate-1.17: .......... done
[123amd64-default-build-as-user-job-03] Extracting htslib-1.16: .......... done
=====
Message from ca_root_nss-3.87:
--
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-1.0.5_1 depends on shared library: libhts.so - found (/usr/local/lib/libhts.so)
===> Returning to build of vcflib-1.0.5_1
===> vcflib-1.0.5_1 depends on shared library: libcurl.so - found (/usr/local/lib/libcurl.so)
===========================================================================
=======================<phase: configure >============================
===> Configuring for vcflib-1.0.5_1
===> Performing out-of-source build
/bin/mkdir -p /wrkdirs/usr/ports/biology/vcflib/work/.build
-- The C compiler identification is Clang 10.0.1
-- The CXX compiler identification is Clang 10.0.1
-- 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 "3.9.16", 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 "2.10.3")
-- 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 "1.2.11")
-- Found CURL: /usr/local/lib/libcurl.so (found version "7.87.0")
--
-- Found OpenMP_C: -fopenmp=libomp (found version "4.5")
-- Found OpenMP_CXX: -fopenmp=libomp (found version "4.5")
-- Found OpenMP: TRUE (found version "4.5")
-- 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 - found
-- Found Threads: TRUE
-- Checking for module 'htslib'
-- Found htslib, version 1.16
-- Checking for module 'tabixpp'
-- Package 'tabixpp', required by 'virtual:world', not found
-- /wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.5/contrib/WFA2-lib/lib/libwfa.a
Pandoc needs to be installed to generate the man pages
-- Configuring done
-- Generating done
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
===========================================================================
=======================<phase: build >============================
===> Building for vcflib-1.0.5_1
gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/vcflib/work/.build'
/usr/local/bin/cmake -S/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.5 -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/ZIG-EXT.dir/build.make CMakeFiles/ZIG-EXT.dir/depend
gmake -f CMakeFiles/wfa-EXT.dir/build.make CMakeFiles/wfa-EXT.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-1.0.5 /wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.5 /wrkdirs/usr/ports/biology/vcflib/work/.build /wrkdirs/usr/ports/biology/vcflib/work/.build /wrkdirs/usr/ports/biology/vcflib/work/.build/CMakeFiles/ZIG-EXT.dir/DependInfo.cmake
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-1.0.5 /wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.5 /wrkdirs/usr/ports/biology/vcflib/work/.build /wrkdirs/usr/ports/biology/vcflib/work/.build /wrkdirs/usr/ports/biology/vcflib/work/.build/CMakeFiles/wfa-EXT.dir/DependInfo.cmake
gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/vcflib/work/.build'
gmake -f CMakeFiles/ZIG-EXT.dir/build.make CMakeFiles/ZIG-EXT.dir/build
gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/vcflib/work/.build'
gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/vcflib/work/.build'
gmake -f CMakeFiles/wfa-EXT.dir/build.make CMakeFiles/wfa-EXT.dir/build
gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/vcflib/work/.build'
[ 0%] Creating directories for 'ZIG-EXT'
/usr/local/bin/cmake -Dcfgdir= -P /wrkdirs/usr/ports/biology/vcflib/work/.build/ZIG-EXT-prefix/tmp/ZIG-EXT-mkdirs.cmake
[ 1%] Creating directories for 'wfa-EXT'
/usr/local/bin/cmake -Dcfgdir= -P /wrkdirs/usr/ports/biology/vcflib/work/.build/wfa-EXT-prefix/tmp/wfa-EXT-mkdirs.cmake
/usr/local/bin/cmake -E touch /wrkdirs/usr/ports/biology/vcflib/work/.build/ZIG-EXT-prefix/src/ZIG-EXT-stamp/ZIG-EXT-mkdir
/usr/local/bin/cmake -E touch /wrkdirs/usr/ports/biology/vcflib/work/.build/wfa-EXT-prefix/src/wfa-EXT-stamp/wfa-EXT-mkdir
[ 1%] No download step for 'ZIG-EXT'
/usr/local/bin/cmake -E echo_append
/usr/local/bin/cmake -E touch /wrkdirs/usr/ports/biology/vcflib/work/.build/ZIG-EXT-prefix/src/ZIG-EXT-stamp/ZIG-EXT-download
[ 2%] No download step for 'wfa-EXT'
/usr/local/bin/cmake -E echo_append
[ 2%] No update step for 'ZIG-EXT'
cd /wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.5/src/zig && /usr/local/bin/cmake -E echo_append
/usr/local/bin/cmake -E touch /wrkdirs/usr/ports/biology/vcflib/work/.build/wfa-EXT-prefix/src/wfa-EXT-stamp/wfa-EXT-download
cd /wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.5/src/zig && /usr/local/bin/cmake -E touch /wrkdirs/usr/ports/biology/vcflib/work/.build/ZIG-EXT-prefix/src/ZIG-EXT-stamp/ZIG-EXT-update
[ 3%] No update step for 'wfa-EXT'
cd /wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.5/contrib/WFA2-lib && /usr/local/bin/cmake -E echo_append
[ 4%] No patch step for 'ZIG-EXT'
/usr/local/bin/cmake -E echo_append
cd /wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.5/contrib/WFA2-lib && /usr/local/bin/cmake -E touch /wrkdirs/usr/ports/biology/vcflib/work/.build/wfa-EXT-prefix/src/wfa-EXT-stamp/wfa-EXT-update
/usr/local/bin/cmake -E touch /wrkdirs/usr/ports/biology/vcflib/work/.build/ZIG-EXT-prefix/src/ZIG-EXT-stamp/ZIG-EXT-patch
[ 4%] No patch step for 'wfa-EXT'
/usr/local/bin/cmake -E echo_append
[ 5%] No configure step for 'ZIG-EXT'
/usr/local/bin/cmake -E touch /wrkdirs/usr/ports/biology/vcflib/work/.build/wfa-EXT-prefix/src/wfa-EXT-stamp/wfa-EXT-patch
cd /wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.5/src/zig && /usr/local/bin/cmake -E echo_append
cd /wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.5/src/zig && /usr/local/bin/cmake -E touch /wrkdirs/usr/ports/biology/vcflib/work/.build/ZIG-EXT-prefix/src/ZIG-EXT-stamp/ZIG-EXT-configure
[ 5%] No configure step for 'wfa-EXT'
cd /wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.5/contrib/WFA2-lib && /usr/local/bin/cmake -E echo_append
[ 5%] Performing build step for 'ZIG-EXT'
cd /wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.5/contrib/WFA2-lib && /usr/local/bin/cmake -E touch /wrkdirs/usr/ports/biology/vcflib/work/.build/wfa-EXT-prefix/src/wfa-EXT-stamp/wfa-EXT-configure
cd /wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.5/src/zig && /wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.5/src/zig/compile.sh -Drelease-fast=true -freference-trace
[ 6%] Performing build step for 'wfa-EXT'
cd /wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.5/contrib/WFA2-lib && gmake BUILD_WFA_PARALLEL=1 BUILD_TOOLS=0 BUILD_EXAMPLES=0 CC_FLAGS=-fPIC setup lib_wfa
gmake[4]: Entering directory '/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.5/contrib/WFA2-lib'
gmake --directory=alignment all
gmake[5]: Entering directory '/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.5/contrib/WFA2-lib/alignment'
cc -fPIC -I.. -c affine_penalties.c -o ../build/affine_penalties.o
cc -fPIC -I.. -c affine2p_penalties.c -o ../build/affine2p_penalties.o
cc -fPIC -I.. -c cigar.c -o ../build/cigar.o
cc -fPIC -I.. -c score_matrix.c -o ../build/score_matrix.o
gmake[5]: Leaving directory '/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.5/contrib/WFA2-lib/alignment'
gmake --directory=bindings/cpp all
gmake[5]: Entering directory '/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.5/contrib/WFA2-lib/bindings/cpp'
c++ -fPIC -I../.. -c WFAligner.cpp -o ../../build/cpp/WFAligner.o
In file included from WFAligner.cpp:32:
In file included from ./WFAligner.hpp:37:
In file included from ./../../wavefront/wfa.hpp:35:
In file included from ./../../wavefront/wfa.h:36:
In file included from ./../../wavefront/wavefront_attributes.h:39:
./../system/profiler_timer.h:60:19: error: field has incomplete type 'struct timespec'
struct timespec begin_timer; // Timer begin
^
./../system/profiler_timer.h:53:35: note: forward declaration of 'timespec'
void timer_get_system_time(struct timespec *ts);
^
1 error generated.
gmake[5]: *** [Makefile:23: ../../build/cpp/WFAligner.o] Error 1
gmake[5]: Leaving directory '/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.5/contrib/WFA2-lib/bindings/cpp'
gmake[4]: *** [Makefile:87: bindings/cpp] Error 2
gmake[4]: Leaving directory '/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.5/contrib/WFA2-lib'
gmake[3]: *** [CMakeFiles/wfa-EXT.dir/build.make:89: wfa-EXT-prefix/src/wfa-EXT-stamp/wfa-EXT-build] Error 2
gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/vcflib/work/.build'
gmake[2]: *** [CMakeFiles/Makefile2:290: CMakeFiles/wfa-EXT.dir/all] Error 2
gmake[2]: *** Waiting for unfinished jobs....
[ 7%] No install step for 'ZIG-EXT'
cd /wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.5/src/zig && /usr/local/bin/cmake -E echo_append
[ 7%] Completed 'ZIG-EXT'
/usr/local/bin/cmake -E make_directory /wrkdirs/usr/ports/biology/vcflib/work/.build/CMakeFiles
/usr/local/bin/cmake -E touch /wrkdirs/usr/ports/biology/vcflib/work/.build/CMakeFiles/ZIG-EXT-complete
/usr/local/bin/cmake -E touch /wrkdirs/usr/ports/biology/vcflib/work/.build/ZIG-EXT-prefix/src/ZIG-EXT-stamp/ZIG-EXT-done
gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/vcflib/work/.build'
[ 7%] Built target ZIG-EXT
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