From owner-freebsd-pkg-fallout@FreeBSD.ORG Thu Oct 10 08:16:28 2013 Return-Path: Delivered-To: pkg-fallout@FreeBSD.org Received: from mx1.freebsd.org (mx1.freebsd.org [8.8.178.115]) (using TLSv1 with cipher ADH-AES256-SHA (256/256 bits)) (No client certificate requested) by hub.freebsd.org (Postfix) with ESMTP id 76E2F203; Thu, 10 Oct 2013 08:16:28 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: from beefy1.isc.freebsd.org (beefy1.isc.freebsd.org [IPv6:2001:4f8:3:ffe0:4072:0:16:38]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (No client certificate requested) by mx1.freebsd.org (Postfix) with ESMTPS id 618C628B9; Thu, 10 Oct 2013 08:16:28 +0000 (UTC) Received: from beefy1.isc.freebsd.org (localhost [127.0.0.1]) by beefy1.isc.freebsd.org (8.14.7/8.14.7) with ESMTP id r9A8GS7I093461; Thu, 10 Oct 2013 08:16:28 GMT (envelope-from pkg-fallout@FreeBSD.org) Received: (from root@localhost) by beefy1.isc.freebsd.org (8.14.7/8.14.7/Submit) id r9A8GSEF093456; Thu, 10 Oct 2013 08:16:28 GMT (envelope-from pkg-fallout@FreeBSD.org) Date: Thu, 10 Oct 2013 08:16:28 GMT From: pkg-fallout@FreeBSD.org Message-Id: <201310100816.r9A8GSEF093456@beefy1.isc.freebsd.org> To: makc@FreeBSD.org Subject: [REL - head-i386-default][science/openbabel] Failed for openbabel-2.3.2 in build Cc: pkg-fallout@FreeBSD.org X-BeenThere: freebsd-pkg-fallout@freebsd.org X-Mailman-Version: 2.1.14 Precedence: list List-Id: Fallout logs from package building List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Thu, 10 Oct 2013 08:16:28 -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: makc@FreeBSD.org Last committer: bapt@FreeBSD.org Ident: $FreeBSD: head/science/openbabel/Makefile 327767 2013-09-20 22:48:30Z bapt $ Log URL: http://beefy1.isc.freebsd.org/bulk/head-i386-default/2013-10-10_05h56m46s/logs/openbabel-2.3.2.log Build URL: http://beefy1.isc.freebsd.org/bulk/head-i386-default/2013-10-10_05h56m46s Log: ====>> Building science/openbabel build started at Thu Oct 10 08:16:12 UTC 2013 port directory: /usr/ports/science/openbabel building for: FreeBSD head-i386-default-job-17 10.0-ALPHA5 FreeBSD 10.0-ALPHA5 r256139 i386 maintained by: makc@FreeBSD.org Makefile ident: $FreeBSD: head/science/openbabel/Makefile 327767 2013-09-20 22:48:30Z bapt $ Poudriere version: 3.1-pre ---Begin Environment--- UNAME_m=i386 UNAME_p=i386 OSVERSION=1000055 UNAME_v=FreeBSD 10.0-ALPHA5 r256139 UNAME_r=10.0-ALPHA5 BLOCKSIZE=K MAIL=/var/mail/root PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/games:/usr/local/sbin:/usr/local/bin:/root/bin STATUS=1 MASTERMNT=/usr/local/poudriere/data/build/head-i386-default/ref PKG_EXT=txz tpid=81467 POUDRIERE_BUILD_TYPE=bulk NBPARALLEL=24 PKGNG=1 PKGNAME=openbabel-2.3.2 PKG_DELETE=/usr/local/sbin/pkg-static delete -y -f PKG_ADD=/usr/local/sbin/pkg-static add PWD=/root MASTERNAME=head-i386-default USER=root HOME=/root POUDRIERE_VERSION=3.1-pre LOCALBASE=/usr/local PACKAGE_BUILDING=yes PKG_VERSION=/poudriere/pkg-static version ---End Environment--- ---Begin OPTIONS List--- ===> The following configuration options are available for openbabel-2.3.2: CAIRO=off: PNG support via cairo library PYTHON=on: Python bindings or support ===> Use 'make config' to modify these settings ---End OPTIONS List--- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- TMPDIR="/tmp" TMPDIR="/tmp" PYTHON="/usr/local/bin/python2.7" SHELL=/bin/sh CONFIG_SHELL=/bin/sh --End CONFIGURE_ENV-- --MAKE_ENV-- TMPDIR="/tmp" TMPDIR="/tmp" SHELL=/bin/sh NO_LINT=YES PREFIX=/usr/local LOCALBASE=/usr/local LIBDIR="/usr/lib" CC="cc" CFLAGS="-O2 -pipe -fno-strict-aliasing" CPP="cpp" CPPFLAGS="" LDFLAGS="" CXX="c++" CXXFLAGS="-O2 -pipe -fno-strict-aliasing" MANPREFIX="/usr/local" BSD_INSTALL_PROGRAM="install -s -o root -g wheel -m 555" BSD_INSTALL_LIB="install -s -o root -g wheel -m 444" BSD_INSTALL_SCRIPT="install -o root -g wheel -m 555" BSD_INSTALL_DATA="install -o root -g wheel -m 444" BSD_INSTALL_MAN="install -o root -g wheel -m 444" --End MAKE_ENV-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/openbabel DOCSDIR=/usr/local/share/doc/openbabel EXAMPLESDIR=/usr/local/share/examples/openbabel WWWDIR=/usr/local/www/openbabel ETCDIR=/usr/local/etc/openbabel --End SUB_LIST-- ---Begin make.conf--- ARCH=i386 MACHINE=i386 MACHINE_ARCH=i386 USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PACKAGES=/packages DISTDIR=/distfiles #### /usr/local/etc/poudriere.d/make.conf #### WITH_PKGNG=yes NO_RESTRICTED=yes DISABLE_MAKE_JOBS=yes ---End make.conf--- ===> Cleaning for openbabel-2.3.2 =================================================== =========================================================================== =================================================== ===> openbabel-2.3.2 depends on file: /usr/local/sbin/pkg - not found ===> Verifying install for /usr/local/sbin/pkg in /usr/ports/ports-mgmt/pkg ===> Installing existing package /packages/All/pkg-1.1.4_7.txz Installing pkg-1.1.4_7... done If you are upgrading from the old package format, first run: # pkg2ng ===> Returning to build of openbabel-2.3.2 =========================================================================== =================================================== =========================================================================== =================================================== ===> Fetching all distfiles required by openbabel-2.3.2 for building =========================================================================== =================================================== ===> Fetching all distfiles required by openbabel-2.3.2 for building => SHA256 Checksum OK for openbabel-2.3.2.tar.gz. =========================================================================== =================================================== =========================================================================== =================================================== ===> Fetching all distfiles required by openbabel-2.3.2 for building ===> Extracting for openbabel-2.3.2 => SHA256 Checksum OK for openbabel-2.3.2.tar.gz. =========================================================================== =================================================== =========================================================================== =================================================== ===> Patching for openbabel-2.3.2 ===> Applying FreeBSD patches for openbabel-2.3.2 /usr/bin/sed -i.bak -e '/find_package(Cairo)/d' /wrkdirs/usr/ports/science/openbabel/work/openbabel-2.3.2/CMakeLists.txt /usr/bin/sed -i.bak -e '/pkgconfig/s,${LIB_INSTALL_DIR},libdata,' /wrkdirs/usr/ports/science/openbabel/work/openbabel-2.3.2/CMakeLists.txt /usr/bin/sed -i.bak -e 's,share/man,man,' /wrkdirs/usr/ports/science/openbabel/work/openbabel-2.3.2/doc/CMakeLists.txt =========================================================================== =================================================== ===> openbabel-2.3.2 depends on file: /usr/local/include/eigen3/Eigen/Eigen - not found ===> Verifying install for /usr/local/include/eigen3/Eigen/Eigen in /usr/ports/math/eigen3 ===> Installing existing package /packages/All/eigen-3.2.0.txz Installing eigen-3.2.0... done ===> Returning to build of openbabel-2.3.2 ===> openbabel-2.3.2 depends on file: /usr/local/bin/python2.7 - not found ===> Verifying install for /usr/local/bin/python2.7 in /usr/ports/lang/python27 ===> Installing existing package /packages/All/python27-2.7.5_3.txz Installing python27-2.7.5_3...Installing gettext-0.18.3... done done ==== Note that some of the standard modules are provided as separate ports since they require extra dependencies: bsddb databases/py-bsddb gdbm databases/py-gdbm sqlite3 databases/py-sqlite3 tkinter x11-toolkits/py-tkinter Install them as needed. ==== ===> Returning to build of openbabel-2.3.2 ===> openbabel-2.3.2 depends on executable: python - not found ===> Verifying install for python in /usr/ports/lang/python ===> Installing existing package /packages/All/python-2.7_1,2.txz Installing python-2.7_1,2...Installing python2-2_1... done done ===> Returning to build of openbabel-2.3.2 ===> openbabel-2.3.2 depends on file: /usr/local/bin/cmake - not found ===> Verifying install for /usr/local/bin/cmake in /usr/ports/devel/cmake ===> Installing existing package /packages/All/cmake-2.8.11.2.txz Installing cmake-2.8.11.2...Installing cmake-modules-2.8.11.2_1... done done ===> Returning to build of openbabel-2.3.2 =========================================================================== =================================================== ===> openbabel-2.3.2 depends on shared library: xml2.5 - not found ===> Verifying install for xml2.5 in /usr/ports/textproc/libxml2 ===> Installing existing package /packages/All/libxml2-2.8.0_2.txz Installing libxml2-2.8.0_2... done ===> Returning to build of openbabel-2.3.2 =========================================================================== =================================================== ===> Configuring for openbabel-2.3.2 ===> Performing out-of-source build /bin/mkdir -p /wrkdirs/usr/ports/science/openbabel/work/.build -- The C compiler identification is Clang 3.3.0 -- The CXX compiler identification is Clang 3.3.0 -- 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 -- 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 -- Using included inchi library. -- Found LibXml2: /usr/local/lib/libxml2.so (found version "2.8.0") -- Found ZLIB: /usr/lib/libz.so (found version "1.2.8") -- Could NOT find wxWidgets (missing: wxWidgets_FOUND) -- Looking for conio.h -- Looking for conio.h - not found -- Looking for sys/time.h -- Looking for sys/time.h - found -- Looking for time.h -- Looking for time.h - found -- Looking for strings.h -- Looking for strings.h - found -- Looking for rpc/xdr.h -- Looking for rpc/xdr.h - not found -- Looking for regex.h -- Looking for regex.h - found -- Looking for C++ include sstream -- Looking for C++ include sstream - found -- Looking for rint -- Looking for rint - not found -- Looking for snprintf -- Looking for snprintf - found -- Looking for sranddev -- Looking for sranddev - found -- Looking for strcasecmp -- Looking for strcasecmp - found -- Looking for strncasecmp -- Looking for strncasecmp - found -- Looking for dlopen in dl -- Looking for dlopen in dl - not found -- Looking for sys/types.h -- Looking for sys/types.h - found -- Looking for stdint.h -- Looking for stdint.h - found -- Looking for stddef.h -- Looking for stddef.h - found -- Check size of clock_t -- Check size of clock_t - done -- Performing Test SCANDIR_NEEDS_CONST -- Performing Test SCANDIR_NEEDS_CONST - Failed -- Found Eigen3: /usr/local/include/eigen3 (Required is at least version "2.91.0") -- Could NOT find Cairo. PNG output will NOT be supported. -- Looking for getopt -- Looking for getopt - found -- GUI will not be built -- Found PythonInterp: /usr/local/bin/python2.7 (found suitable version "2.7.5", minimum required is "2.7") -- Found PythonLibs: /usr/local/lib/libpython2.7.so (found suitable version "2.7.5", minimum required is "2.7") -- Python bindings will be compiled -- Configuring done -- Generating done CMake Warning: Manually-specified variables were not used by the project: CMAKE_CXX_FLAGS_DEBUG CMAKE_C_FLAGS_DEBUG THREADS_HAVE_PTHREAD_ARG -- Build files have been written to: /wrkdirs/usr/ports/science/openbabel/work/.build =========================================================================== =================================================== ===> Building for openbabel-2.3.2 /usr/local/bin/cmake -H/wrkdirs/usr/ports/science/openbabel/work/openbabel-2.3.2 -B/wrkdirs/usr/ports/science/openbabel/work/.build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/local/bin/cmake -E cmake_progress_start /wrkdirs/usr/ports/science/openbabel/work/.build/CMakeFiles /wrkdirs/usr/ports/science/openbabel/work/.build/CMakeFiles/progress.marks /usr/bin/make -f CMakeFiles/Makefile2 all /usr/bin/make -f src/CMakeFiles/openbabel.dir/build.make src/CMakeFiles/openbabel.dir/depend cd /wrkdirs/usr/ports/science/openbabel/work/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /wrkdirs/usr/ports/science/openbabel/work/openbabel-2.3.2 /wrkdirs/usr/ports/science/openbabel/work/openbabel-2.3.2/src /wrkdirs/usr/ports/science/openbabel/work/.build /wrkdirs/usr/ports/science/openbabel/work/.build/src /wrkdirs/usr/ports/science/openbabel/work/.build/src/CMakeFiles/openbabel.dir/DependInfo.cmake Scanning dependencies of target openbabel /usr/bin/make -f src/CMakeFiles/openbabel.dir/build.make src/CMakeFiles/openbabel.dir/build /usr/local/bin/cmake -E cmake_progress_report /wrkdirs/usr/ports/science/openbabel/work/.build/CMakeFiles [ 0%] Building CXX object src/CMakeFiles/openbabel.dir/alias.o cd /wrkdirs/usr/ports/science/openbabel/work/.build/src && /usr/bin/c++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_SHARED_POINTER -DMAKE_OBDLL -DUSING_DYNAMIC_LIBS -O2 -pipe -fno-strict-aliasing -O2 -pipe -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/science/openbabel/work/.build/include -I/wrkdirs/usr/ports/science/openbabel/work/openbabel-2.3.2/data -I/wrkdirs/usr/ports/science/openbabel/work/openbabel-2.3.2/include -I/usr/local/include/eigen3 -DOB_MODULE_PATH="\"/usr/local/lib/openbabel/2.3.2\"" -o CMakeFiles/openbabel.dir/alias.o -c /wrkdirs/usr/ports/science/openbabel/work/openbabel-2.3.2/src/alias.cpp In file included from /wrkdirs/usr/ports/science/openbabel/work/openbabel-2.3.2/src/alias.cpp:17: In file included from /wrkdirs/usr/ports/science/openbabel/work/openbabel-2.3.2/include/openbabel/alias.h:19: /wrkdirs/usr/ports/science/openbabel/work/openbabel-2.3.2/include/openbabel/shared_ptr.h:27:14: error: no member named 'tr1' in namespace 'std' using std::tr1::shared_ptr; ~~~~~^ In file included from /wrkdirs/usr/ports/science/openbabel/work/openbabel-2.3.2/src/alias.cpp:17: /wrkdirs/usr/ports/science/openbabel/work/openbabel-2.3.2/include/openbabel/alias.h:118:47: error: no template named 'shared_ptr'; did you mean 'std::shared_ptr'? typedef std::vector< std::pair > > SmartsTable; ^~~~~~~~~~ std::shared_ptr /usr/include/c++/v1/memory:3817:24: note: 'std::shared_ptr' declared here class _LIBCPP_TYPE_VIS shared_ptr ^ 2 errors generated. *** Error code 1 Stop. make[3]: stopped in /wrkdirs/usr/ports/science/openbabel/work/.build *** Error code 1 Stop. make[2]: stopped in /wrkdirs/usr/ports/science/openbabel/work/.build *** Error code 1 Stop. make[1]: stopped in /wrkdirs/usr/ports/science/openbabel/work/.build *** Error code 1 Stop. make: stopped in /usr/ports/science/openbabel ===> Cleaning for openbabel-2.3.2