[package - head-armv6-default][biology/seqan-apps] Failed for seqan-apps-2.2.0 in configure
pkg-fallout at FreeBSD.org
pkg-fallout at FreeBSD.org
Sun Sep 25 20:28:52 UTC 2016
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: h2+fbsdports at fsfe.org
Last committer: pawel at FreeBSD.org
Ident: $FreeBSD: head/biology/seqan-apps/Makefile 422156 2016-09-14 19:38:58Z pawel $
Log URL: http://beefy8.nyi.freebsd.org/data/head-armv6-default/p422472_s306008/logs/seqan-apps-2.2.0.log
Build URL: http://beefy8.nyi.freebsd.org/build.html?mastername=head-armv6-default&build=p422472_s306008
Log:
====>> Building biology/seqan-apps
build started at Sun Sep 25 20:26:47 UTC 2016
port directory: /usr/ports/biology/seqan-apps
building for: FreeBSD head-armv6-default-job-19 12.0-CURRENT FreeBSD 12.0-CURRENT r306008 arm
maintained by: h2+fbsdports at fsfe.org
Makefile ident: $FreeBSD: head/biology/seqan-apps/Makefile 422156 2016-09-14 19:38:58Z pawel $
Poudriere version: 3.1.14
Host OSVERSION: 1200005
Jail OSVERSION: 1200008
!!! Jail is newer than host. (Jail: 1200008, Host: 1200005) !!!
!!! This is not supported. !!!
!!! Host kernel must be same or newer than jail. !!!
!!! Expect build failures. !!!
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---End Environment---
---Begin OPTIONS List---
---End OPTIONS List---
--CONFIGURE_ARGS--
--End CONFIGURE_ARGS--
--CONFIGURE_ENV--
XDG_DATA_HOME=/wrkdirs/usr/ports/biology/seqan-apps/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/seqan-apps/work HOME=/wrkdirs/usr/ports/biology/seqan-apps/work TMPDIR="/tmp" SHELL=/bin/sh CONFIG_SHELL=/bin/sh
--End CONFIGURE_ENV--
--MAKE_ENV--
XDG_DATA_HOME=/wrkdirs/usr/ports/biology/seqan-apps/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/seqan-apps/work HOME=/wrkdirs/usr/ports/biology/seqan-apps/work TMPDIR="/tmp" NO_PIE=yes MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES ADDR2LINE="/usr/local/bin/addr2line" AR="/usr/local/bin/ar" AS="/usr/local/bin/as" CPPFILT="/usr/local/bin/c++filt" GPROF="/usr/local/bin/gprof" LD="/usr/local/bin/ld" NM="/usr/local/bin/nm" OBJCOPY="/usr/local/bin/objcopy" OBJDUMP="/usr/local/bin/objdump" RANLIB="/usr/local/bin/ranlib" READELF="/usr/local/bin/readelf" SIZE="/usr/local/bin/size" STRINGS="/usr/local/bin/strings" PREFIX=/usr/local LOCALBASE=/usr/local LIBDIR="/usr/lib" CC="gcc49" CFLAGS="-O2 -pipe -Wl,-rpath=/usr/local/lib/gcc49 -fno-strict-aliasing" CPP="cpp49" CPPFLAGS="" LDFLAGS=" -Wl,-rpath=/usr/local/lib/gcc49 -L/usr/local/lib/gcc49" LIBS="" CXX="g++49" CXXFLAGS="-O2 -pipe -Wl,-rpath=/usr/local/lib/gcc49 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc4
9" MANPREFIX="/usr/local" BSD_INSTALL_PROGRAM="install -s -m 555" BSD_INSTALL_LIB="install -s -m 444" BSD_INSTALL_SCRIPT="install -m 555" BSD_INSTALL_DATA="install -m 0644" BSD_INSTALL_MAN="install -m 444"
--End MAKE_ENV--
--PLIST_SUB--
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RM_I386=""
OSREL=12.0
PREFIX=%D
LOCALBASE=/usr/local
RESETPREFIX=/usr/local
PORTDOCS=""
PORTEXAMPLES=""
LIB32DIR=lib
DOCSDIR="share/doc/seqan-apps"
EXAMPLESDIR="share/examples/seqan-apps"
DATADIR="share/seqan-apps"
WWWDIR="www/seqan-apps"
ETCDIR="etc/seqan-apps"
--End PLIST_SUB--
--SUB_LIST--
PREFIX=/usr/local
LOCALBASE=/usr/local
DATADIR=/usr/local/share/seqan-apps
DOCSDIR=/usr/local/share/doc/seqan-apps
EXAMPLESDIR=/usr/local/share/examples/seqan-apps
WWWDIR=/usr/local/www/seqan-apps
ETCDIR=/usr/local/etc/seqan-apps
--End SUB_LIST--
---Begin make.conf---
CC=/nxb-bin/usr/bin/cc
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OBJCOPY=/nxb-bin/usr/bin/objcopy
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YACC=/nxb-bin/usr/bin/yacc
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MAKE=/nxb-bin/usr/bin/make
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MAKE=/nxb-bin/usr/bin/make
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YACC=/nxb-bin/usr/bin/yacc
NM=/nxb-bin/usr/bin/nm
MAKE=/nxb-bin/usr/bin/make
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AWK=/nxb-bin/usr/bin/awk
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CC=/nxb-bin/usr/bin/cc
CPP=/nxb-bin/usr/bin/cpp
CXX=/nxb-bin/usr/bin/c++
AS=/nxb-bin/usr/bin/as
NM=/nxb-bin/usr/bin/nm
<snip>
PACKAGES=/packages
DISTDIR=/distfiles
MACHINE=arm
MACHINE_ARCH=armv6
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
DISABLE_MAKE_JOBS=poudriere
---End make.conf---
---Begin make.nxb.conf---
CC=/nxb-bin/usr/bin/cc
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LD=/nxb-bin/usr/bin/ld
OBJCOPY=/nxb-bin/usr/bin/objcopy
SIZE=/nxb-bin/usr/bin/size
STRIPBIN=/nxb-bin/usr/bin/strip
SED=/nxb-bin/usr/bin/sed
READELF=/nxb-bin/usr/bin/readelf
RANLIB=/nxb-bin/usr/bin/ranlib
YACC=/nxb-bin/usr/bin/yacc
MAKE=/nxb-bin/usr/bin/make
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FLEX=/nxb-bin/usr/bin/flex
---End make.nxb.conf---
=======================<phase: check-sanity >============================
===> License BSD3CLAUSE LGPL3 GPLv3 accepted by the user
===========================================================================
=======================<phase: pkg-depends >============================
===> seqan-apps-2.2.0 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-1.8.7_3.txz
[head-armv6-default-job-19] Installing pkg-1.8.7_3...
[head-armv6-default-job-19] Extracting pkg-1.8.7_3: .......... done
===> seqan-apps-2.2.0 depends on file: /usr/local/sbin/pkg - found
===> Returning to build of seqan-apps-2.2.0
===========================================================================
=======================<phase: fetch-depends >============================
===========================================================================
=======================<phase: fetch >============================
===> License BSD3CLAUSE LGPL3 GPLv3 accepted by the user
=> seqan-seqan-seqan-v2.2.0_GH0.tar.gz doesn't seem to exist in /portdistfiles/.
=> Attempting to fetch https://codeload.github.com/seqan/seqan/tar.gz/seqan-v2.2.0?dummy=/seqan-seqan-seqan-v2.2.0_GH0.tar.gz
fetch: https://codeload.github.com/seqan/seqan/tar.gz/seqan-v2.2.0?dummy=/seqan-seqan-seqan-v2.2.0_GH0.tar.gz: size unknown
fetch: https://codeload.github.com/seqan/seqan/tar.gz/seqan-v2.2.0?dummy=/seqan-seqan-seqan-v2.2.0_GH0.tar.gz: size of remote file is not known
seqan-seqan-seqan-v2.2.0_GH0.tar.gz 0 B 0 Bps
===> Fetching all distfiles required by seqan-apps-2.2.0 for building
===========================================================================
=======================<phase: checksum >============================
===> License BSD3CLAUSE LGPL3 GPLv3 accepted by the user
===> Fetching all distfiles required by seqan-apps-2.2.0 for building
=> SHA256 Checksum OK for seqan-seqan-seqan-v2.2.0_GH0.tar.gz.
===========================================================================
=======================<phase: extract-depends>============================
===========================================================================
=======================<phase: extract >============================
===> License BSD3CLAUSE LGPL3 GPLv3 accepted by the user
===> Fetching all distfiles required by seqan-apps-2.2.0 for building
===> Extracting for seqan-apps-2.2.0
=> SHA256 Checksum OK for seqan-seqan-seqan-v2.2.0_GH0.tar.gz.
===========================================================================
=======================<phase: patch-depends >============================
===========================================================================
=======================<phase: patch >============================
===> Patching for seqan-apps-2.2.0
===========================================================================
=======================<phase: build-depends >============================
===> seqan-apps-2.2.0 depends on package: boost-libs>0 - not found
===> Installing existing package /packages/All/boost-libs-1.55.0_12.txz
[head-armv6-default-job-19] Installing boost-libs-1.55.0_12...
[head-armv6-default-job-19] `-- Installing icu-55.1,1...
[head-armv6-default-job-19] `-- Extracting icu-55.1,1: .......... done
[head-armv6-default-job-19] Extracting boost-libs-1.55.0_12: .......... done
Message from boost-libs-1.55.0_12:
You have built the Boost library with thread support.
Don't forget to add -pthread to your linker options when
linking your code.
===> seqan-apps-2.2.0 depends on package: boost-libs>0 - found
===> Returning to build of seqan-apps-2.2.0
===> seqan-apps-2.2.0 depends on file: /usr/local/bin/cmake - not found
===> Installing existing package /packages/All/cmake-3.6.2.txz
[head-armv6-default-job-19] Installing cmake-3.6.2...
[head-armv6-default-job-19] `-- Installing expat-2.2.0...
[head-armv6-default-job-19] `-- Extracting expat-2.2.0: .......... done
[head-armv6-default-job-19] `-- Installing cmake-modules-3.6.2...
[head-armv6-default-job-19] `-- Extracting cmake-modules-3.6.2: .......... done
[head-armv6-default-job-19] `-- Installing curl-7.50.1...
[head-armv6-default-job-19] | `-- Installing ca_root_nss-3.26...
[head-armv6-default-job-19] | `-- Extracting ca_root_nss-3.26: ....... done
[head-armv6-default-job-19] `-- Extracting curl-7.50.1: .......... done
[head-armv6-default-job-19] `-- Installing libarchive-3.2.1,1...
[head-armv6-default-job-19] | `-- Installing liblz4-131...
[head-armv6-default-job-19] | `-- Extracting liblz4-131: .......... done
[head-armv6-default-job-19] | `-- Installing lzo2-2.09...
[head-armv6-default-job-19] | `-- Extracting lzo2-2.09: .......... done
[head-armv6-default-job-19] `-- Extracting libarchive-3.2.1,1: .......... done
[head-armv6-default-job-19] `-- Installing jsoncpp-1.7.3...
[head-armv6-default-job-19] `-- Extracting jsoncpp-1.7.3: .......... done
[head-armv6-default-job-19] Extracting cmake-3.6.2: .......... done
Message from ca_root_nss-3.26:
********************************* 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
***************************************************************************
===> seqan-apps-2.2.0 depends on file: /usr/local/bin/cmake - found
===> Returning to build of seqan-apps-2.2.0
===> seqan-apps-2.2.0 depends on executable: gcc49 - not found
===> Installing existing package /packages/All/gcc49-4.9.4.txz
[head-armv6-default-job-19] Installing gcc49-4.9.4...
[head-armv6-default-job-19] `-- Installing indexinfo-0.2.5...
[head-armv6-default-job-19] `-- Extracting indexinfo-0.2.5: .... done
[head-armv6-default-job-19] `-- Installing mpc-1.0.3...
[head-armv6-default-job-19] | `-- Installing gmp-5.1.3_3...
[head-armv6-default-job-19] | `-- Extracting gmp-5.1.3_3: .......... done
[head-armv6-default-job-19] | `-- Installing mpfr-3.1.4...
[head-armv6-default-job-19] | `-- Extracting mpfr-3.1.4: .......... done
[head-armv6-default-job-19] `-- Extracting mpc-1.0.3: ...... done
[head-armv6-default-job-19] `-- Installing binutils-2.27_3,1...
[head-armv6-default-job-19] | `-- Installing gettext-runtime-0.19.8.1...
[head-armv6-default-job-19] | `-- Extracting gettext-runtime-0.19.8.1: .......... done
[head-armv6-default-job-19] `-- Extracting binutils-2.27_3,1: .......... done
[head-armv6-default-job-19] Extracting gcc49-4.9.4: .......... done
Message from gcc49-4.9.4:
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/gcc49
For ports leveraging USE_GCC, USES=compiler, or USES=fortran this happens
transparently.
===> seqan-apps-2.2.0 depends on executable: gcc49 - found
===> Returning to build of seqan-apps-2.2.0
===> seqan-apps-2.2.0 depends on file: /usr/local/bin/as - found
===========================================================================
=======================<phase: lib-depends >============================
===========================================================================
=======================<phase: configure >============================
===> Configuring for seqan-apps-2.2.0
===> Performing out-of-source build
/bin/mkdir -p /wrkdirs/usr/ports/biology/seqan-apps/work/.build
-- The CXX compiler identification is GNU 4.9.4
-- Check for working CXX compiler: /usr/local/bin/g++49
-- Check for working CXX compiler: /usr/local/bin/g++49 -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Initializing SeqAn Build System...
-- Selected repository dir: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.2.0
-- No revision system found.
-- Repository date not determined.
-- Repository revision not determined.
-- Configuring apps
-- Configuring apps/alf
-- Performing Test CXX14_BUILTIN
-- Performing Test CXX14_BUILTIN - Failed
-- Performing Test CXX14_FLAG
CMake Error: Generator: execution of make failed. Make command was: "/usr/bin/make" "cmTC_4bf05/fast"
-- Performing Test CXX14_FLAG - Failed
CMake Error at util/cmake/FindSeqAn.cmake:187 (message):
SeqAn requires C++14 since v2.2.0, but your compiler does not support it.
Call Stack (most recent call first):
apps/alf/CMakeLists.txt:20 (find_package)
-- Configuring incomplete, errors occurred!
See also "/wrkdirs/usr/ports/biology/seqan-apps/work/.build/CMakeFiles/CMakeOutput.log".
See also "/wrkdirs/usr/ports/biology/seqan-apps/work/.build/CMakeFiles/CMakeError.log".
*** Error code 1
Stop.
make: stopped in /usr/ports/biology/seqan-apps
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