Date: Sat, 31 Oct 2015 20:23:51 GMT From: pkg-fallout@FreeBSD.org To: pkg-fallout@FreeBSD.org Subject: [package - head-armv6-default][biology/seqan] Failed for seqan-1.3.1_3 in configure Message-ID: <201510312023.t9VKNprE086626@beefy8.nyi.freebsd.org>
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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/p400328_s290048/logs/seqan-1.3.1_3.log Build URL: http://beefy8.nyi.freebsd.org/build.html?mastername=head-armv6-default&build=p400328_s290048 Log: ====>> Building biology/seqan build started at Sat Oct 31 20:21:11 UTC 2015 port directory: /usr/ports/biology/seqan building for: FreeBSD head-armv6-default-job-24 11.0-CURRENT FreeBSD 11.0-CURRENT r290048 arm maintained by: h2+fbsdports@fsfe.org Makefile ident: $FreeBSD: head/biology/seqan/Makefile 381791 2015-03-21 11:53:27Z marino $ Poudriere version: 3.1.9 Host OSVERSION: 1100079 Jail OSVERSION: 1100083 !!! Jail is newer than host. (Jail: 1100083, Host: 1100079) !!! !!! 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 OSVERSION=1100083 UNAME_v=FreeBSD 11.0-CURRENT r290048 UNAME_r=11.0-CURRENT LC_COLLATE=C BLOCKSIZE=K MAIL=/var/mail/root STATUS=1 SAVED_TERM=screen MASTERMNT=/usr/local/poudriere/data/.m/head-armv6-default/ref PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin POUDRIERE_BUILD_TYPE=bulk PKGNAME=seqan-1.3.1_3 OLDPWD=/ PWD=/usr/local/poudriere/data/.m/head-armv6-default/ref/.p/pool MASTERNAME=head-armv6-default SCRIPTPREFIX=/usr/local/share/poudriere USER=root HOME=/root POUDRIERE_VERSION=3.1.9 SCRIPTPATH=/usr/local/share/poudriere/bulk.sh LIBEXECPREFIX=/usr/local/libexec/poudriere LOCALBASE=/usr/local PACKAGE_BUILDING=yes ---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 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-aliasing -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_VERSION=python2.7 PYTHON_VER=2.7 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 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 <snip> 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 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 ---End make.nxb.conf--- =======================<phase: check-sanity >============================ ===> License BSD3CLAUSE GPLv3 accepted by the user =========================================================================== =======================<phase: pkg-depends >============================ ===> seqan-1.3.1_3 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.6.1_1.txz [head-armv6-default-job-24] Installing pkg-1.6.1_1... [head-armv6-default-job-24] Extracting pkg-1.6.1_1: .......... done Message from pkg-1.6.1_1: If you are upgrading from the old package format, first run: # pkg2ng ===> seqan-1.3.1_3 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of seqan-1.3.1_3 =========================================================================== =======================<phase: fetch-depends >============================ =========================================================================== =======================<phase: fetch >============================ ===> License BSD3CLAUSE GPLv3 accepted by the user ===> Fetching all distfiles required by seqan-1.3.1_3 for building =========================================================================== =======================<phase: checksum >============================ ===> 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. =========================================================================== =======================<phase: extract-depends>============================ =========================================================================== =======================<phase: extract >============================ ===> 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. =========================================================================== =======================<phase: patch-depends >============================ =========================================================================== =======================<phase: patch >============================ ===> Patching for seqan-1.3.1_3 ===> Applying FreeBSD patches for seqan-1.3.1_3 =========================================================================== =======================<phase: build-depends >============================ ===> seqan-1.3.1_3 depends on file: /usr/local/bin/cmake - not found ===> Installing existing package /packages/All/cmake-3.3.1.txz [head-armv6-default-job-24] Installing cmake-3.3.1... [head-armv6-default-job-24] `-- Installing expat-2.1.0_3... [head-armv6-default-job-24] `-- Extracting expat-2.1.0_3: .......... done [head-armv6-default-job-24] `-- Installing cmake-modules-3.3.1... [head-armv6-default-job-24] `-- Extracting cmake-modules-3.3.1: .......... done [head-armv6-default-job-24] `-- Installing curl-7.45.0... [head-armv6-default-job-24] | `-- Installing ca_root_nss-3.20... [head-armv6-default-job-24] | `-- Extracting ca_root_nss-3.20: ....... done [head-armv6-default-job-24] `-- Extracting curl-7.45.0: .......... done [head-armv6-default-job-24] `-- Installing libarchive-3.1.2_4,1... [head-armv6-default-job-24] | `-- Installing lzo2-2.09... [head-armv6-default-job-24] | `-- Extracting lzo2-2.09: .......... done [head-armv6-default-job-24] `-- Extracting libarchive-3.1.2_4,1: .......... done [head-armv6-default-job-24] `-- Installing jsoncpp-0.6.0.r2_2... [head-armv6-default-job-24] `-- Extracting jsoncpp-0.6.0.r2_2: .......... done [head-armv6-default-job-24] Extracting cmake-3.3.1: .......... done Message from ca_root_nss-3.20: ********************************* 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/python27-2.7.10_1.txz [head-armv6-default-job-24] Installing python27-2.7.10_1... [head-armv6-default-job-24] `-- Installing libffi-3.2.1... [head-armv6-default-job-24] | `-- Installing indexinfo-0.2.4... [head-armv6-default-job-24] | `-- Extracting indexinfo-0.2.4: .... done [head-armv6-default-job-24] `-- Extracting libffi-3.2.1: .......... done [head-armv6-default-job-24] `-- Installing gettext-runtime-0.19.6... [head-armv6-default-job-24] `-- Extracting gettext-runtime-0.19.6: .......... done [head-armv6-default-job-24] `-- Installing readline-6.3.8... [head-armv6-default-job-24] `-- Extracting readline-6.3.8: .......... done [head-armv6-default-job-24] Extracting python27-2.7.10_1: .......... done Message from python27-2.7.10_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.txz [head-armv6-default-job-24] Installing gcc-4.8.5... [head-armv6-default-job-24] `-- Installing mpc-1.0.3... [head-armv6-default-job-24] | `-- Installing gmp-5.1.3_2... [head-armv6-default-job-24] | `-- Extracting gmp-5.1.3_2: .......... done [head-armv6-default-job-24] | `-- Installing mpfr-3.1.2_2... [head-armv6-default-job-24] | `-- Extracting mpfr-3.1.2_2: .......... done [head-armv6-default-job-24] `-- Extracting mpc-1.0.3: ...... done [head-armv6-default-job-24] `-- Installing binutils-2.25.1... [head-armv6-default-job-24] `-- Extracting binutils-2.25.1: .......... done [head-armv6-default-job-24] Extracting gcc-4.8.5: .......... done Message from gcc-4.8.5: 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 =========================================================================== =======================<phase: lib-depends >============================ =========================================================================== =======================<phase: configure >============================ ===> 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 CMake Error: Generator: execution of make failed. Make command was: "/usr/bin/make" "cmTC_dde06/fast" -- Detecting C compile features - failed -- 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 "2.7.10") 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 -- Performing Test TR1_SHARED_PTR_USE_TR1_MEMORY - Success -- 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
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