[REL - head-i386-default][science/openbabel] Failed for openbabel-2.3.2 in build
pkg-fallout at FreeBSD.org
pkg-fallout at FreeBSD.org
Thu Oct 24 15:02:02 UTC 2013
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 at FreeBSD.org
Last committer: makc at FreeBSD.org
Ident: $FreeBSD: head/science/openbabel/Makefile 330663 2013-10-17 18:49:09Z makc $
Log URL: http://beefy1.isc.freebsd.org/bulk/head-i386-default/2013-10-24_12h59m17s/logs/openbabel-2.3.2.log
Build URL: http://beefy1.isc.freebsd.org/bulk/head-i386-default/2013-10-24_12h59m17s
Log:
====>> Building science/openbabel
build started at Thu Oct 24 15:01:46 UTC 2013
port directory: /usr/ports/science/openbabel
building for: FreeBSD head-i386-default-job-12 11.0-CURRENT FreeBSD 11.0-CURRENT r256430 i386
maintained by: makc at FreeBSD.org
Makefile ident: $FreeBSD: head/science/openbabel/Makefile 330663 2013-10-17 18:49:09Z makc $
Poudriere version: 3.1-pre
---Begin Environment---
UNAME_m=i386
UNAME_p=i386
OSVERSION=1100000
UNAME_v=FreeBSD 11.0-CURRENT r256430
UNAME_r=11.0-CURRENT
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=52122
POUDRIERE_BUILD_TYPE=bulk
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
PKG_BIN=/usr/local/sbin/pkg-static
---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
PORTSDIR=/usr/ports
PACKAGES=/packages
DISTDIR=/distfiles
#### /usr/local/etc/poudriere.d/make.conf ####
WITH_PKGNG=yes
NO_RESTRICTED=yes
DISABLE_MAKE_JOBS=poudriere
---End make.conf---
===> Cleaning for openbabel-2.3.2
=======================<phase: check-config >============================
===========================================================================
=======================<phase: pkg-depends >============================
===> 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_8.txz
Installing pkg-1.1.4_8... done
If you are upgrading from the old package format, first run:
# pkg2ng
===> Returning to build of openbabel-2.3.2
===========================================================================
=======================<phase: fetch-depends >============================
===========================================================================
=======================<phase: fetch >============================
===> Fetching all distfiles required by openbabel-2.3.2 for building
===========================================================================
=======================<phase: checksum >============================
===> Fetching all distfiles required by openbabel-2.3.2 for building
=> SHA256 Checksum OK for openbabel-2.3.2.tar.gz.
===========================================================================
=======================<phase: extract-depends>============================
===========================================================================
=======================<phase: extract >============================
===> 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.
===========================================================================
=======================<phase: patch-depends >============================
===========================================================================
=======================<phase: patch >============================
===> 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
===========================================================================
=======================<phase: build-depends >============================
===> 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-0.18.3.1... 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
===========================================================================
=======================<phase: lib-depends >============================
===> 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
===========================================================================
=======================<phase: configure >============================
===> 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
===========================================================================
=======================<phase: 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<std::string, shared_ptr<OBSmartsPattern> > > 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
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