[package - 112i386-default][biology/hhsuite] Failed for hhsuite-3.2.0 in configure
pkg-fallout at FreeBSD.org
pkg-fallout at FreeBSD.org
Tue May 21 03:24:00 UTC 2019
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: yuri at FreeBSD.org
Last committer: yuri at FreeBSD.org
Ident: $FreeBSD: head/biology/hhsuite/Makefile 502015 2019-05-19 06:52:38Z yuri $
Log URL: http://beefy10.nyi.freebsd.org/data/112i386-default/502184/logs/hhsuite-3.2.0.log
Build URL: http://beefy10.nyi.freebsd.org/build.html?mastername=112i386-default&build=502184
Log:
=>> Building biology/hhsuite
build started at Tue May 21 03:23:32 UTC 2019
port directory: /usr/ports/biology/hhsuite
package name: hhsuite-3.2.0
building for: FreeBSD 112i386-default-job-15 11.2-RELEASE-p10 FreeBSD 11.2-RELEASE-p10 i386
maintained by: yuri at FreeBSD.org
Makefile ident: $FreeBSD: head/biology/hhsuite/Makefile 502015 2019-05-19 06:52:38Z yuri $
Poudriere version: 3.2.8-4-g701d8fe1
Host OSVERSION: 1300018
Jail OSVERSION: 1102000
Job Id: 15
---Begin Environment---
SHELL=/bin/csh
UNAME_p=i386
UNAME_m=i386
OSVERSION=1102000
UNAME_v=FreeBSD 11.2-RELEASE-p10
UNAME_r=11.2-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=3.2.8-4-g701d8fe1
MASTERMNT=/usr/local/poudriere/data/.m/112i386-default/ref
POUDRIERE_BUILD_TYPE=bulk
PACKAGE_BUILDING=yes
SAVED_TERM=
PWD=/usr/local/poudriere/data/.m/112i386-default/ref/.p/pool
P_PORTS_FEATURES=FLAVORS SELECTED_OPTIONS
MASTERNAME=112i386-default
SCRIPTPREFIX=/usr/local/share/poudriere
OLDPWD=/usr/local/poudriere/data/.m/112i386-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---
---End OPTIONS List---
--MAINTAINER--
yuri at FreeBSD.org
--End MAINTAINER--
--CONFIGURE_ARGS--
--End CONFIGURE_ARGS--
--CONFIGURE_ENV--
ac_cv_path_PERL=/usr/local/bin/perl ac_cv_path_PERL_PATH=/usr/local/bin/perl PERL_USE_UNSAFE_INC=1 PYTHON="/usr/local/bin/python3.6" XDG_DATA_HOME=/wrkdirs/usr/ports/biology/hhsuite/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/hhsuite/work HOME=/wrkdirs/usr/ports/biology/hhsuite/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/hhsuite/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin SHELL=/bin/sh CONFIG_SHELL=/bin/sh
--End CONFIGURE_ENV--
--MAKE_ENV--
PERL_USE_UNSAFE_INC=1 XDG_DATA_HOME=/wrkdirs/usr/ports/biology/hhsuite/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/hhsuite/work HOME=/wrkdirs/usr/ports/biology/hhsuite/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/hhsuite/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin NO_PIE=yes MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES DESTDIR=/wrkdirs/usr/ports/biology/hhsuite/work/stage PREFIX=/usr/local LOCALBASE=/usr/local CC="cc" CFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " CPP="cpp" CPPFLAGS="" LDFLAGS=" -Wl,-rpath,/usr/local/mpi/openmpi/lib -L/usr/local/mpi/openmpi/lib -lmpi -fstack-protector-strong " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " MANPREFIX="/usr/local" BSD_INSTALL_PROGRAM="install -s -m 555" BSD_INSTALL_LIB="install -s -m 0644" BSD_INSTALL_SCRIPT="install -m 555" BSD_INSTALL_DATA="install -m 0644" BSD_INSTALL_MAN="install -m 444"
--End MAKE_ENV--
--PLIST_SUB--
CMAKE_BUILD_TYPE="release" PYTHON_INCLUDEDIR=include/python3.6m PYTHON_LIBDIR=lib/python3.6 PYTHON_PLATFORM=freebsd11 PYTHON_SITELIBDIR=lib/python3.6/site-packages PYTHON_SUFFIX=36 PYTHON_VER=3.6 PYTHON_VERSION=python3.6 PYTHON2="@comment " PYTHON3="" OSREL=11.2 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib PERL_VERSION=5.28.2 PERL_VER=5.28 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/5.28 DOCSDIR="share/doc/hhsuite" EXAMPLESDIR="share/examples/hhsuite" DATADIR="share/hhsuite" WWWDIR="www/hhsuite" ETCDIR="etc/hhsuite"
--End PLIST_SUB--
--SUB_LIST--
PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/hhsuite DOCSDIR=/usr/local/share/doc/hhsuite EXAMPLESDIR=/usr/local/share/examples/hhsuite WWWDIR=/usr/local/www/hhsuite ETCDIR=/usr/local/etc/hhsuite
--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=i386
MACHINE_ARCH=i386
ARCH=${MACHINE_ARCH}
#### /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
# stable/10 includes src.conf too late but make.conf is in sys.mk
.if ${.CURDIR:M/poudriere/jails/10*/usr/src/usr.bin/xlint*}
# Disable build of llib now that head no longer has lint(1)
LINT= true
.endif
#### /usr/ports/Mk/Scripts/ports_env.sh ####
_CCVERSION_921dbbb2=FreeBSD clang version 6.0.0 (tags/RELEASE_600/final 326565) (based on LLVM 6.0.0) Target: i386-unknown-freebsd11.2 Thread model: posix InstalledDir: /usr/bin
_ALTCCVERSION_921dbbb2=none
_CXXINTERNAL_acaad9ca=FreeBSD clang version 6.0.0 (tags/RELEASE_600/final 326565) (based on LLVM 6.0.0) Target: i386-unknown-freebsd11.2 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" "-m" "elf_i386_fbsd" "-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_b2657cc3=yes
CC_OUTPUT_921dbbb2_380987f7=yes
CC_OUTPUT_921dbbb2_160933ec=yes
CC_OUTPUT_921dbbb2_fb62803b=yes
_OBJC_CCVERSION_921dbbb2=FreeBSD clang version 6.0.0 (tags/RELEASE_600/final 326565) (based on LLVM 6.0.0) Target: i386-unknown-freebsd11.2 Thread model: posix InstalledDir: /usr/bin
_OBJC_ALTCCVERSION_921dbbb2=none
ARCH=i386
OPSYS=FreeBSD
_OSRELEASE=11.2-RELEASE-p10
OSREL=11.2
OSVERSION=1102000
PYTHONBASE=/usr/local
CONFIGURE_MAX_CMD_LEN=262144
HAVE_PORTS_ENV=1
#### Misc Poudriere ####
GID=0
UID=0
DISABLE_MAKE_JOBS=poudriere
---End make.conf---
--Resource limits--
cpu time (seconds, -t) unlimited
file size (512-blocks, -f) unlimited
data seg size (kbytes, -d) 524288
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) 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 GPLv3 accepted by the user
===========================================================================
=======================<phase: pkg-depends >============================
===> hhsuite-3.2.0 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-1.10.5_5.txz
[112i386-default-job-15] Installing pkg-1.10.5_5...
[112i386-default-job-15] Extracting pkg-1.10.5_5: .......... done
===> hhsuite-3.2.0 depends on file: /usr/local/sbin/pkg - found
===> Returning to build of hhsuite-3.2.0
===========================================================================
=======================<phase: fetch-depends >============================
===========================================================================
=======================<phase: fetch >============================
===> License GPLv3 accepted by the user
=> soedinglab-hh-suite-v3.2.0_GH0.tar.gz doesn't seem to exist in /portdistfiles/.
=> Attempting to fetch https://codeload.github.com/soedinglab/hh-suite/tar.gz/v3.2.0?dummy=/soedinglab-hh-suite-v3.2.0_GH0.tar.gz
soedinglab-hh-suite-v3.2.0_GH0.tar.gz 0 B 0 Bps
===> Fetching all distfiles required by hhsuite-3.2.0 for building
===========================================================================
=======================<phase: checksum >============================
===> License GPLv3 accepted by the user
===> Fetching all distfiles required by hhsuite-3.2.0 for building
=> SHA256 Checksum OK for soedinglab-hh-suite-v3.2.0_GH0.tar.gz.
===========================================================================
=======================<phase: extract-depends>============================
===========================================================================
=======================<phase: extract >============================
===> License GPLv3 accepted by the user
===> Fetching all distfiles required by hhsuite-3.2.0 for building
===> Extracting for hhsuite-3.2.0
=> SHA256 Checksum OK for soedinglab-hh-suite-v3.2.0_GH0.tar.gz.
===========================================================================
=======================<phase: patch-depends >============================
===========================================================================
=======================<phase: patch >============================
===> Patching for hhsuite-3.2.0
===> Applying FreeBSD patches for hhsuite-3.2.0
===========================================================================
=======================<phase: build-depends >============================
===> hhsuite-3.2.0 depends on package: openmpi>0 - not found
===> Installing existing package /packages/All/openmpi-1.10.7_5.txz
[112i386-default-job-15] Installing openmpi-1.10.7_5...
[112i386-default-job-15] `-- Installing gcc8-8.3.0_2...
[112i386-default-job-15] | `-- Installing binutils-2.32,1...
[112i386-default-job-15] | | `-- Installing gettext-runtime-0.19.8.1_2...
<snip>
[112i386-default-job-15] `-- Extracting libltdl-2.4.6: .......... done
[112i386-default-job-15] `-- Installing slurm-wlm-18.08.7...
[112i386-default-job-15] | `-- Installing hdf-szip-2.1.1...
[112i386-default-job-15] | `-- Extracting hdf-szip-2.1.1: .......... done
[112i386-default-job-15] | `-- Installing hdf5-1.10.5_1...
[112i386-default-job-15] | `-- Extracting hdf5-1.10.5_1: .......... done
[112i386-default-job-15] | `-- Installing json-c-0.13.1...
[112i386-default-job-15] | `-- Extracting json-c-0.13.1: .......... done
[112i386-default-job-15] | `-- Installing liblz4-1.9.1,1...
[112i386-default-job-15] | `-- Extracting liblz4-1.9.1,1: .......... done
[112i386-default-job-15] | `-- Installing libsysinfo-0.0.3_2...
[112i386-default-job-15] | `-- Extracting libsysinfo-0.0.3_2: ......... done
[112i386-default-job-15] | `-- Installing lua52-5.2.4...
[112i386-default-job-15] | | `-- Installing libedit-3.1.20181209_2,1...
[112i386-default-job-15] | | `-- Extracting libedit-3.1.20181209_2,1: .......... done
[112i386-default-job-15] | `-- Extracting lua52-5.2.4: ......... done
[112i386-default-job-15] | `-- Installing munge-0.5.13_1...
[112i386-default-job-15] | | `-- Installing perl5-5.28.2...
[112i386-default-job-15] | | `-- Extracting perl5-5.28.2: .......... done
[112i386-default-job-15] | `-- Extracting munge-0.5.13_1: ......... done
[112i386-default-job-15] | `-- Installing readline-8.0.0...
[112i386-default-job-15] | `-- Extracting readline-8.0.0: .......... done
===> Creating groups.
Creating group 'slurm' with gid '468'.
===> Creating users
Creating user 'slurm' with uid '468'.
[112i386-default-job-15] `-- Extracting slurm-wlm-18.08.7: .......... done
[112i386-default-job-15] Extracting openmpi-1.10.7_5: .......... done
Message from gcc8-8.3.0_2:
To ensure binaries built with this toolchain find appropriate versions
of the necessary run-time libraries, you may want to link using
-Wl,-rpath=/usr/local/lib/gcc8
For ports leveraging USE_GCC, USES=compiler, or USES=fortran this happens
transparently.
Message from perl5-5.28.2:
The /usr/bin/perl symlink has been removed starting with Perl 5.20.
For shebangs, you should either use:
#!/usr/local/bin/perl
or
#!/usr/bin/env perl
The first one will only work if you have a /usr/local/bin/perl,
the second will work as long as perl is in PATH.
===> hhsuite-3.2.0 depends on package: openmpi>0 - found
===> Returning to build of hhsuite-3.2.0
===> hhsuite-3.2.0 depends on file: /usr/local/bin/cmake - not found
===> Installing existing package /packages/All/cmake-3.14.4.txz
[112i386-default-job-15] Installing cmake-3.14.4...
[112i386-default-job-15] `-- Installing curl-7.64.1_1...
[112i386-default-job-15] | `-- Installing ca_root_nss-3.44...
[112i386-default-job-15] | `-- Extracting ca_root_nss-3.44: ........ done
[112i386-default-job-15] | `-- Installing libnghttp2-1.38.0...
[112i386-default-job-15] | `-- Extracting libnghttp2-1.38.0: .......... done
[112i386-default-job-15] `-- Extracting curl-7.64.1_1: .......... done
[112i386-default-job-15] `-- Installing expat-2.2.6_1...
[112i386-default-job-15] `-- Extracting expat-2.2.6_1: .......... done
[112i386-default-job-15] `-- Installing jsoncpp-1.8.1_6...
[112i386-default-job-15] `-- Extracting jsoncpp-1.8.1_6: .......... done
[112i386-default-job-15] `-- Installing libarchive-3.3.3,1...
[112i386-default-job-15] | `-- Installing lzo2-2.10_1...
[112i386-default-job-15] | `-- Extracting lzo2-2.10_1: .......... done
[112i386-default-job-15] `-- Extracting libarchive-3.3.3,1: .......... done
[112i386-default-job-15] `-- Installing libuv-1.29.0...
[112i386-default-job-15] `-- Extracting libuv-1.29.0: .......... done
[112i386-default-job-15] `-- Installing rhash-1.3.5...
[112i386-default-job-15] `-- Extracting rhash-1.3.5: .......... done
[112i386-default-job-15] Extracting cmake-3.14.4: .......... done
Message from ca_root_nss-3.44:
********************************* WARNING *********************************
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.
*********************************** NOTE **********************************
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
***************************************************************************
===> hhsuite-3.2.0 depends on file: /usr/local/bin/cmake - found
===> Returning to build of hhsuite-3.2.0
===> hhsuite-3.2.0 depends on executable: ninja - not found
===> Installing existing package /packages/All/ninja-1.9.0,2.txz
[112i386-default-job-15] Installing ninja-1.9.0,2...
[112i386-default-job-15] `-- Installing python36-3.6.8_2...
[112i386-default-job-15] | `-- Installing libffi-3.2.1_3...
[112i386-default-job-15] | `-- Extracting libffi-3.2.1_3: .......... done
[112i386-default-job-15] `-- Extracting python36-3.6.8_2: .......... done
[112i386-default-job-15] Extracting ninja-1.9.0,2: ......... done
Message from python36-3.6.8_2:
===========================================================================
Note that some standard Python modules are provided as separate ports
as they require additional dependencies. They are available as:
py36-gdbm databases/py-gdbm at py36
py36-sqlite3 databases/py-sqlite3 at py36
py36-tkinter x11-toolkits/py-tkinter at py36
===========================================================================
===> hhsuite-3.2.0 depends on executable: ninja - found
===> Returning to build of hhsuite-3.2.0
===> hhsuite-3.2.0 depends on file: /usr/local/bin/python3.6 - found
===> hhsuite-3.2.0 depends on package: perl5>=5.28.r1<5.29 - found
===========================================================================
=======================<phase: lib-depends >============================
===> hhsuite-3.2.0 depends on shared library: libomp.so - not found
===> Installing existing package /packages/All/openmp-8.0.0_1.txz
[112i386-default-job-15] Installing openmp-8.0.0_1...
[112i386-default-job-15] Extracting openmp-8.0.0_1: .......... done
Message from openmp-8.0.0_1:
===> NOTICE:
This port is deprecated; you may wish to reconsider installing it:
Part of base system since FreeBSD 11.3/12.1.
It is scheduled to be removed on or after 2019-12-31.
===> hhsuite-3.2.0 depends on shared library: libomp.so - found (/usr/local/lib/libomp.so)
===> Returning to build of hhsuite-3.2.0
===========================================================================
=======================<phase: configure >============================
===> Configuring for hhsuite-3.2.0
===> Performing out-of-source build
/bin/mkdir -p /wrkdirs/usr/ports/biology/hhsuite/work/.build
-- The C compiler identification is Clang 6.0.0
-- The CXX compiler identification is Clang 6.0.0
-- Check for working C compiler: /usr/bin/cc
-- Check for working C compiler: /usr/bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Check for working CXX compiler: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Looking for fmemopen
-- Looking for fmemopen - found
-- Found MPI_C: /usr/local/mpi/openmpi/lib/libmpi.so (found version "3.0")
-- Found MPI_CXX: /usr/local/mpi/openmpi/lib/libmpi_cxx.so (found version "3.0")
-- Found MPI: TRUE (found version "3.0")
-- xxd not found, using xxdi.pl instead
-- Performing Test HAVE_MM_MALLOC
-- Performing Test HAVE_MM_MALLOC - Success
-- Performing Test HAVE_POSIX_MEMALIGN
-- Performing Test HAVE_POSIX_MEMALIGN - Success
-- Performing Test HAVE_AVX2_EXTENSIONS
-- Performing Test HAVE_AVX2_EXTENSIONS - Failed
-- Performing Test HAVE_AVX_EXTENSIONS
-- Performing Test HAVE_AVX_EXTENSIONS - Failed
-- Performing Test HAVE_SSE4_2_EXTENSIONS
-- Performing Test HAVE_SSE4_2_EXTENSIONS - Failed
-- Performing Test HAVE_SSE4_1_EXTENSIONS
-- Performing Test HAVE_SSE4_1_EXTENSIONS - Failed
-- Performing Test HAVE_SSSE3_EXTENSIONS
-- Performing Test HAVE_SSSE3_EXTENSIONS - Failed
-- Performing Test HAVE_SSE3_EXTENSIONS
-- Performing Test HAVE_SSE3_EXTENSIONS - Failed
-- Performing Test HAVE_SSE2_EXTENSIONS
-- Performing Test HAVE_SSE2_EXTENSIONS - Failed
-- Performing Test HAVE_SSE_EXTENSIONS
-- Performing Test HAVE_SSE_EXTENSIONS - Failed
CMake Error at src/CMakeLists.txt:18 (message):
At least SSE2 instruction set support is required! CMake will exit.
-- Configuring incomplete, errors occurred!
See also "/wrkdirs/usr/ports/biology/hhsuite/work/.build/CMakeFiles/CMakeOutput.log".
See also "/wrkdirs/usr/ports/biology/hhsuite/work/.build/CMakeFiles/CMakeError.log".
*** Error code 1
Stop.
make: stopped in /usr/ports/biology/hhsuite
More information about the freebsd-pkg-fallout
mailing list