From owner-freebsd-pkg-fallout@freebsd.org Fri Mar 11 12:57:00 2016 Return-Path: Delivered-To: freebsd-pkg-fallout@mailman.ysv.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2001:1900:2254:206a::19:1]) by mailman.ysv.freebsd.org (Postfix) with ESMTP id 41A0FACCA84 for ; Fri, 11 Mar 2016 12:57:00 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: from mailman.ysv.freebsd.org (mailman.ysv.freebsd.org [IPv6:2001:1900:2254:206a::50:5]) by mx1.freebsd.org (Postfix) with ESMTP id 2FC419AF for ; Fri, 11 Mar 2016 12:57:00 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: by mailman.ysv.freebsd.org (Postfix) id 2C7EEACCA82; Fri, 11 Mar 2016 12:57:00 +0000 (UTC) Delivered-To: pkg-fallout@mailman.ysv.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2001:1900:2254:206a::19:1]) by mailman.ysv.freebsd.org (Postfix) with ESMTP id 12367ACCA80 for ; Fri, 11 Mar 2016 12:57:00 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: from beefy8.nyi.freebsd.org (beefy8.nyi.freebsd.org [IPv6:2610:1c1:1:6080::16:eb]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (Client did not present a certificate) by mx1.freebsd.org (Postfix) with ESMTPS id CF6529AE for ; Fri, 11 Mar 2016 12:56:59 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: from beefy8.nyi.freebsd.org (localhost [127.0.0.1]) by beefy8.nyi.freebsd.org (8.15.2/8.15.2) with ESMTP id u2BCuwOM090529 for ; Fri, 11 Mar 2016 12:56:58 GMT (envelope-from pkg-fallout@FreeBSD.org) Received: (from root@localhost) by beefy8.nyi.freebsd.org (8.15.2/8.15.2/Submit) id u2BCuwti090528; Fri, 11 Mar 2016 12:56:58 GMT (envelope-from pkg-fallout@FreeBSD.org) Date: Fri, 11 Mar 2016 12:56:58 GMT From: pkg-fallout@FreeBSD.org Message-Id: <201603111256.u2BCuwti090528@beefy8.nyi.freebsd.org> To: pkg-fallout@FreeBSD.org Subject: [package - head-armv6-default][biology/seqan] Failed for seqan-1.3.1_3 in configure X-BeenThere: freebsd-pkg-fallout@freebsd.org X-Mailman-Version: 2.1.21 Precedence: list List-Id: Fallout logs from package building List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Fri, 11 Mar 2016 12:57:00 -0000 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@fsfe.org Last committer: marino@FreeBSD.org Ident: $FreeBSD: head/biology/seqan/Makefile 381791 2015-03-21 11:53:27Z marino $ Log URL: http://beefy8.nyi.freebsd.org/data/head-armv6-default/p410528_s296455/logs/seqan-1.3.1_3.log Build URL: http://beefy8.nyi.freebsd.org/build.html?mastername=head-armv6-default&build=p410528_s296455 Log: ====>> Building biology/seqan build started at Fri Mar 11 12:54:32 UTC 2016 port directory: /usr/ports/biology/seqan building for: FreeBSD head-armv6-default-job-05 11.0-CURRENT FreeBSD 11.0-CURRENT r296455 arm maintained by: h2+fbsdports@fsfe.org Makefile ident: $FreeBSD: head/biology/seqan/Makefile 381791 2015-03-21 11:53:27Z marino $ Poudriere version: 3.1.12 Host OSVERSION: 1100100 Jail OSVERSION: 1100101 !!! Jail is newer than host. (Jail: 1100101, Host: 1100100) !!! !!! This is not supported. !!! !!! Host kernel must be same or newer than jail. !!! !!! Expect build failures. !!! ---Begin Environment--- SHELL=/bin/csh UNAME_p=armv6 UNAME_m=arm ABI_FILE=/usr/lib/crt1.o UNAME_v=FreeBSD 11.0-CURRENT r296455 UNAME_r=11.0-CURRENT BLOCKSIZE=K MAIL=/var/mail/root STATUS=1 OPSYS=FreeBSD ARCH=armv6 LINUX_OSRELEASE=2.6.32 SAVED_TERM=screen QEMU_EMULATING=1 MASTERMNT=/usr/local/poudriere/data/.m/head-armv6-default/ref UID=0 PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin _JAVA_VERSION_LIST_REGEXP=1.6\|1.7\|1.8\|1.6+\|1.7+\|1.8+ POUDRIERE_BUILD_TYPE=bulk PKGNAME=seqan-1.3.1_3 OSREL=11.0 _OSRELEASE=11.0-CURRENT PYTHONBASE=/usr/local OLDPWD=/ _SMP_CPUS=24 PWD=/usr/local/poudriere/data/.m/head-armv6-default/ref/.p/pool MASTERNAME=head-armv6-default SCRIPTPREFIX=/usr/local/share/poudriere _JAVA_VENDOR_LIST_REGEXP=openjdk\|oracle\|sun USER=root HOME=/root POUDRIERE_VERSION=3.1.12 SCRIPTPATH=/usr/local/share/poudriere/bulk.sh CONFIGURE_MAX_CMD_LEN=262144 LIBEXECPREFIX=/usr/local/libexec/poudriere LOCALBASE=/usr/local PACKAGE_BUILDING=yes _JAVA_OS_LIST_REGEXP=native\|linux OSVERSION=1100101 ---End Environment--- ---Begin OPTIONS List--- ---End OPTIONS List--- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- PYTHON="/usr/local/bin/python2.7" XDG_DATA_HOME=/wrkdirs/usr/ports/biology/seqan/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/seqan/work HOME=/wrkdirs/usr/ports/biology/seqan/work TMPDIR="/tmp" SHELL=/bin/sh CONFIG_SHELL=/bin/sh --End CONFIGURE_ENV-- --MAKE_ENV-- XDG_DATA_HOME=/wrkdirs/usr/ports/biology/seqan/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/seqan/work HOME=/wrkdirs/usr/ports/biology/seqan/work TMPDIR="/tmp" NO_PIE=yes WITHOUT_DEBUG_FILES=yes WITHOUT_KERNEL_SYMBOLS=yes 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="gcc48" CFLAGS="-O2 -pipe -mfloat-abi=softfp -Wl,-rpath=/usr/local/lib/gcc48 -fno-strict-aliasing" CPP="cpp48" CPPFLAGS="" LDFLAGS=" -Wl,-rpath=/usr/local/lib/gcc48 -L/usr/local/lib/gcc48" LIBS="" CXX="g++48" CXXFLAGS="-O2 -pipe -mfloat-abi=softfp -Wl,-rpath=/usr/local/lib/gcc48 -fno-strict-alias ing -Wl,-rpath=/usr/local/lib/gcc48" 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-- CMAKE_BUILD_TYPE="release" PYTHON_INCLUDEDIR=include/python2.7 PYTHON_LIBDIR=lib/python2.7 PYTHON_PLATFORM=freebsd11 PYTHON_SITELIBDIR=lib/python2.7/site-packages PYTHON_VER=2.7 PYTHON_VERSION=python2.7 OSREL=11.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local PORTDOCS="" PORTEXAMPLES="" LIB32DIR=lib DOCSDIR="share/doc/seqan" EXAMPLESDIR="share/examples/seqan" DATADIR="share/seqan" WWWDIR="www/seqan" ETCDIR="etc/seqan" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/seqan DOCSDIR=/usr/local/share/doc/seqan EXAMPLESDIR=/usr/local/share/examples/seqan WWWDIR=/usr/local/www/seqan ETCDIR=/usr/local/etc/seqan --End SUB_LIST-- ---Begin make.conf--- 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 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 NM=/nxb-bin/usr/bin/nm MAKE=/nxb-bin/usr/bin/make STRINGS=/nxb-bin/usr/bin/strings AWK=/nxb-bin/usr/bin/awk FLEX=/nxb-bin/usr/bin/flex 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 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 NM=/nxb-bin/usr/bin/nm MAKE=/nxb-bin/usr/bin/make STRINGS=/nxb-bin/usr/bin/strings AWK=/nxb-bin/usr/bin/awk FLEX=/nxb-bin/usr/bin/flex 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 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 NM=/nxb-bin/usr/bin/nm MAKE=/nxb-bin/usr/bin/make STRINGS=/nxb-bin/usr/bin/strings AWK=/nxb-bin/usr/bin/awk FLEX=/nxb-bin/usr/bin/flex 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 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 NM=/nxb-bin/usr/bin/nm MAKE=/nxb-bin/usr/bin/make STRINGS=/nxb-bin/usr/bin/strings AWK=/nxb-bin/usr/bin/awk FLEX=/nxb-bin/usr/bin/flex 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 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 NM=/nxb-bin/usr/bin/nm MAKE=/nxb-bin/usr/bin/make STRINGS=/nxb-bin/usr/bin/strings AWK=/nxb-bin/usr/bin/awk .sinclude "/etc/make.nxb.conf" USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles #### /usr/local/etc/poudriere.d/make.conf #### DISABLE_MAKE_JOBS=poudriere ---End make.conf--- ---Begin make.nxb.conf--- 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 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 STRINGS=/nxb-bin/usr/bin/strings AWK=/nxb-bin/usr/bin/awk FLEX=/nxb-bin/usr/bin/flex ---End make.nxb.conf--- =================================================== ===> License BSD3CLAUSE GPLv3 accepted by the user =========================================================================== =================================================== ===> seqan-1.3.1_3 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.6.4_1.txz [head-armv6-default-job-05] Installing pkg-1.6.4_1... [head-armv6-default-job-05] Extracting pkg-1.6.4_1: .......... done ===> seqan-1.3.1_3 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of seqan-1.3.1_3 =========================================================================== =================================================== =========================================================================== =================================================== ===> License BSD3CLAUSE GPLv3 accepted by the user ===> Fetching all distfiles required by seqan-1.3.1_3 for building =========================================================================== =================================================== ===> License BSD3CLAUSE GPLv3 accepted by the user ===> Fetching all distfiles required by seqan-1.3.1_3 for building => SHA256 Checksum OK for seqan-1.3.1.zip. =========================================================================== =================================================== =========================================================================== =================================================== ===> License BSD3CLAUSE GPLv3 accepted by the user ===> Fetching all distfiles required by seqan-1.3.1_3 for building ===> Extracting for seqan-1.3.1_3 => SHA256 Checksum OK for seqan-1.3.1.zip. =========================================================================== =================================================== =========================================================================== =================================================== ===> Patching for seqan-1.3.1_3 ===> Applying FreeBSD patches for seqan-1.3.1_3 =========================================================================== =================================================== ===> seqan-1.3.1_3 depends on file: /usr/local/bin/cmake - not found ===> Installing existing package /packages/All/cmake-3.4.2.txz [head-armv6-default-job-05] Installing cmake-3.4.2... [head-armv6-default-job-05] `-- Installing expat-2.1.0_3... [head-armv6-default-job-05] `-- Extracting expat-2.1.0_3: .......... done [head-armv6-default-job-05] `-- Installing cmake-modules-3.4.2... [head-armv6-default-job-05] `-- Extracting cmake-modules-3.4.2: .......... done [head-armv6-default-job-05] `-- Installing curl-7.47.1... [head-armv6-default-job-05] | `-- Installing ca_root_nss-3.22.2... [head-armv6-default-job-05] | `-- Extracting ca_root_nss-3.22.2: ....... done [head-armv6-default-job-05] `-- Extracting curl-7.47.1: .......... done [head-armv6-default-job-05] `-- Installing libarchive-3.1.2_6,1... [head-armv6-default-job-05] | `-- Installing lzo2-2.09... [head-armv6-default-job-05] | `-- Extracting lzo2-2.09: .......... done [head-armv6-default-job-05] `-- Extracting libarchive-3.1.2_6,1: .......... done [head-armv6-default-job-05] `-- Installing jsoncpp-0.6.0.r2_2... [head-armv6-default-job-05] `-- Extracting jsoncpp-0.6.0.r2_2: .......... done [head-armv6-default-job-05] Extracting cmake-3.4.2: .......... done Message from ca_root_nss-3.22.2: ********************************* 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-1.3.1_3 depends on file: /usr/local/bin/cmake - found ===> Returning to build of seqan-1.3.1_3 ===> seqan-1.3.1_3 depends on file: /usr/local/bin/python2.7 - not found ===> Installing existing package /packages/All/python27-2.7.11_1.txz [head-armv6-default-job-05] Installing python27-2.7.11_1... [head-armv6-default-job-05] `-- Installing libffi-3.2.1... [head-armv6-default-job-05] | `-- Installing indexinfo-0.2.4... [head-armv6-default-job-05] | `-- Extracting indexinfo-0.2.4: .... done [head-armv6-default-job-05] `-- Extracting libffi-3.2.1: .......... done [head-armv6-default-job-05] `-- Installing gettext-runtime-0.19.7... [head-armv6-default-job-05] `-- Extracting gettext-runtime-0.19.7: .......... done [head-armv6-default-job-05] `-- Installing readline-6.3.8... [head-armv6-default-job-05] `-- Extracting readline-6.3.8: .......... done [head-armv6-default-job-05] Extracting python27-2.7.11_1: .......... done Message from python27-2.7.11_1: =========================================================================== Note that some standard Python modules are provided as separate ports as they require additional dependencies. They are available as: bsddb databases/py-bsddb gdbm databases/py-gdbm sqlite3 databases/py-sqlite3 tkinter x11-toolkits/py-tkinter =========================================================================== ===> seqan-1.3.1_3 depends on file: /usr/local/bin/python2.7 - found ===> Returning to build of seqan-1.3.1_3 ===> seqan-1.3.1_3 depends on executable: gcc48 - not found ===> Installing existing package /packages/All/gcc-4.8.5_2.txz [head-armv6-default-job-05] Installing gcc-4.8.5_2... [head-armv6-default-job-05] `-- Installing mpc-1.0.3... [head-armv6-default-job-05] | `-- Installing gmp-5.1.3_3... [head-armv6-default-job-05] | `-- Extracting gmp-5.1.3_3: .......... done [head-armv6-default-job-05] | `-- Installing mpfr-3.1.3_1... [head-armv6-default-job-05] | `-- Extracting mpfr-3.1.3_1: .......... done [head-armv6-default-job-05] `-- Extracting mpc-1.0.3: ...... done [head-armv6-default-job-05] `-- Installing binutils-2.25.1,1... [head-armv6-default-job-05] `-- Extracting binutils-2.25.1,1: .......... done [head-armv6-default-job-05] Extracting gcc-4.8.5_2: .......... done Message from gcc-4.8.5_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/gcc48 For ports leveraging USE_GCC, USES=compiler, or USES=fortran this happens transparently. ===> seqan-1.3.1_3 depends on executable: gcc48 - found ===> Returning to build of seqan-1.3.1_3 ===> seqan-1.3.1_3 depends on file: /usr/local/bin/as - found =========================================================================== =================================================== =========================================================================== =================================================== ===> Configuring for seqan-1.3.1_3 ===> Performing out-of-source build /bin/mkdir -p /wrkdirs/usr/ports/biology/seqan/work/.build -- The C compiler identification is GNU 4.8.5 -- The CXX compiler identification is GNU 4.8.5 -- Check for working C compiler: /usr/local/bin/gcc48 -- Check for working C compiler: /usr/local/bin/gcc48 -- 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/local/bin/g++48 -- Check for working CXX compiler: /usr/local/bin/g++48 -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Detecting CXX compile features -- Detecting CXX compile features - done -- Found PythonInterp: /usr/local/bin/python2.7 (found version "2.7.11") Determining GCC version. GCC version is g++48 (FreeBSD Ports Collection) 4.8.5 Copyright (C) 2015 Free Software Foundation, Inc. This is free software see the source for copying conditions. There is NO warranty not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. -- Performing Test TR1_SHARED_PTR_USE_TR1_MEMORY CMake Error: Generator: execution of make failed. Make command was: "/usr/bin/make" "cmTC_fef33/fast" -- Performing Test TR1_SHARED_PTR_USE_TR1_MEMORY - Failed -- Performing Test TR1_SHARED_PTR_USE_MEMORY -- Performing Test TR1_SHARED_PTR_USE_MEMORY - Failed -- Configuring incomplete, errors occurred! See also "/wrkdirs/usr/ports/biology/seqan/work/.build/CMakeFiles/CMakeOutput.log". See also "/wrkdirs/usr/ports/biology/seqan/work/.build/CMakeFiles/CMakeError.log". *** Error code 1 Stop. make: stopped in /usr/ports/biology/seqan