[package - head-armv6-default][biology/libsbml] Failed for libsbml-5.13.0 in configure

Thu Apr 21 13:56:47 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:     ports at FreeBSD.org
Last committer: mi at FreeBSD.org
Ident:          $FreeBSD: head/biology/libsbml/Makefile 413410 2016-04-16 01:54:15Z mi $
Log URL:        http://beefy8.nyi.freebsd.org/data/head-armv6-default/p413605_s298221/logs/libsbml-5.13.0.log
Build URL:      http://beefy8.nyi.freebsd.org/build.html?mastername=head-armv6-default&build=p413605_s298221
Log:

====>> Building biology/libsbml
build started at Thu Apr 21 13:55:19 UTC 2016
port directory: /usr/ports/biology/libsbml
building for: FreeBSD head-armv6-default-job-20 11.0-CURRENT FreeBSD 11.0-CURRENT r298221 arm
maintained by: ports at FreeBSD.org
Makefile ident:      $FreeBSD: head/biology/libsbml/Makefile 413410 2016-04-16 01:54:15Z mi $
Poudriere version: 3.1.12
Host OSVERSION: 1100102
Jail OSVERSION: 1100105

!!! Jail is newer than host. (Jail: 1100105, Host: 1100102) !!!
!!! 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 r298221
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=libsbml-5.13.0
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=1100105
---End Environment---

---Begin OPTIONS List---
===> The following configuration options are available for libsbml-5.13.0:
     EXAMPLES=on: Build and/or install examples
     PYTHON=off: Python bindings or support
     RUBY=off: Ruby bindings or support
===> Use 'make config' to modify these settings
---End OPTIONS List---

--CONFIGURE_ARGS--

--End CONFIGURE_ARGS--

--CONFIGURE_ENV--
XDG_DATA_HOME=/wrkdirs/usr/ports/biology/libsbml/work  XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/libsbml/work  HOME=/wrkdirs/usr/ports/biology/libsbml/work TMPDIR="/tmp" SHELL=/bin/sh CONFIG_SHELL=/bin/sh
--End CONFIGURE_ENV--

--MAKE_ENV--
XDG_DATA_HOME=/wrkdirs/usr/ports/biology/libsbml/work  XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/libsbml/work  HOME=/wrkdirs/usr/ports/biology/libsbml/work TMPDIR="/tmp" NO_PIE=yes WITHOUT_DEBUG_FILES=yes WITHOUT_KERNEL_SYMBOLS=yes SHELL=/bin/sh NO_LINT=YES PREFIX=/usr/local  LOCALBASE=/usr/local  LIBDIR="/usr/lib"  CC="/nxb-bin/usr/bin/cc" CFLAGS="-O2 -pipe -mfloat-abi=softfp  -I/usr/include -fno-strict-aliasing"  CPP="/nxb-bin/usr/bin/cpp" CPPFLAGS=""  LDFLAGS=" -L/usr/lib" LIBS=""  CXX="/nxb-bin/usr/bin/c++" CXXFLAGS="-O2 -pipe -mfloat-abi=softfp -I/usr/include -fno-strict-aliasing "  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--
PORTVERSION=5.13.0
EXAMPLES=""
NO_EXAMPLES="@comment
"
PYTHON="@comment
"
NO_PYTHON=""
RUBY="@comment
"
NO_RUBY=""
CMAKE_BUILD_TYPE="release"
GTK2_VERSION="2.10.0"
GTK3_VERSION="3.0.0"
OSREL=11.0
PREFIX=%D
LOCALBASE=/usr/local
RESETPREFIX=/usr/local
PORTDOCS=""
PORTEXAMPLES=""
LIB32DIR=lib
DOCSDIR="share/doc/libsbml"
EXAMPLESDIR="share/examples/libsbml"
DATADIR="share/libsbml"
WWWDIR="www/libsbml"
ETCDIR="etc/libsbml"
--End PLIST_SUB--

--SUB_LIST--
EXAMPLES=""
NO_EXAMPLES="@comment
"
PYTHON="@comment
"
NO_PYTHON=""
RUBY="@comment
"
NO_RUBY=""
PREFIX=/usr/local
LOCALBASE=/usr/local
DATADIR=/usr/local/share/libsbml
DOCSDIR=/usr/local/share/doc/libsbml
EXAMPLESDIR=/usr/local/share/examples/libsbml
WWWDIR=/usr/local/www/libsbml
ETCDIR=/usr/local/etc/libsbml
--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
<snip>

===>  License LGPL21 accepted by the user
===> Fetching all distfiles required by libsbml-5.13.0 for building
=> SHA256 Checksum OK for libSBML-5.13.0-core-src.tar.gz.
===========================================================================
=======================<phase: extract-depends>============================
===========================================================================
=======================<phase: extract        >============================
===>   NOTICE:

The libsbml port currently does not have a maintainer. As a result, it is
more likely to have unresolved issues, not be up-to-date, or even be removed in
the future. To volunteer to maintain this port, please create an issue at:

https://bugs.freebsd.org/bugzilla

More information about port maintainership is available at:

https://www.freebsd.org/doc/en/articles/contributing/ports-contributing.html#maintain-port

===>  License LGPL21 accepted by the user
===> Fetching all distfiles required by libsbml-5.13.0 for building
===>  Extracting for libsbml-5.13.0
=> SHA256 Checksum OK for libSBML-5.13.0-core-src.tar.gz.
===========================================================================
=======================<phase: patch-depends  >============================
===========================================================================
=======================<phase: patch          >============================
===>  Patching for libsbml-5.13.0
===========================================================================
=======================<phase: build-depends  >============================
===>   libsbml-5.13.0 depends on file: /usr/local/bin/cmake - not found
===>   Installing existing package /packages/All/cmake-3.5.2.txz
[head-armv6-default-job-20] Installing cmake-3.5.2...
[head-armv6-default-job-20] `-- Installing expat-2.1.0_3...
[head-armv6-default-job-20] `-- Extracting expat-2.1.0_3: .......... done
[head-armv6-default-job-20] `-- Installing cmake-modules-3.5.2...
[head-armv6-default-job-20] `-- Extracting cmake-modules-3.5.2: .......... done
[head-armv6-default-job-20] `-- Installing curl-7.48.0_2...
[head-armv6-default-job-20] |   `-- Installing ca_root_nss-3.22.2...
[head-armv6-default-job-20] |   `-- Extracting ca_root_nss-3.22.2: ....... done
[head-armv6-default-job-20] `-- Extracting curl-7.48.0_2: .......... done
[head-armv6-default-job-20] `-- Installing libarchive-3.1.2_6,1...
[head-armv6-default-job-20] |   `-- Installing lzo2-2.09...
[head-armv6-default-job-20] |   `-- Extracting lzo2-2.09: .......... done
[head-armv6-default-job-20] `-- Extracting libarchive-3.1.2_6,1: .......... done
[head-armv6-default-job-20] `-- Installing jsoncpp-0.6.0.r2_2...
[head-armv6-default-job-20] `-- Extracting jsoncpp-0.6.0.r2_2: .......... done
[head-armv6-default-job-20] Extracting cmake-3.5.2: .......... 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

***************************************************************************
===>   libsbml-5.13.0 depends on file: /usr/local/bin/cmake - found
===>   Returning to build of libsbml-5.13.0
===========================================================================
=======================<phase: lib-depends    >============================
===>   libsbml-5.13.0 depends on shared library: libxml2.so - not found
===>   Installing existing package /packages/All/libxml2-2.9.3.txz
[head-armv6-default-job-20] Installing libxml2-2.9.3...
[head-armv6-default-job-20] Extracting libxml2-2.9.3: .......... done
===>   libsbml-5.13.0 depends on shared library: libxml2.so - found (/usr/local/lib/libxml2.so)
===>   Returning to build of libsbml-5.13.0
===========================================================================
=======================<phase: configure      >============================
===>  Configuring for libsbml-5.13.0
===>   FreeBSD 10 autotools fix applied to /wrkdirs/usr/ports/biology/libsbml/work/libsbml-5.13.0/config/libtool.m4
===>   FreeBSD 10 autotools fix applied to /wrkdirs/usr/ports/biology/libsbml/work/libsbml-5.13.0/configure
===>  Performing out-of-source build
/bin/mkdir -p /wrkdirs/usr/ports/biology/libsbml/work/.build
-- The C compiler identification is Clang 3.8.0
-- The CXX compiler identification is Clang 3.8.0
-- Check for working C compiler: /nxb-bin/usr/bin/cc
-- Check for working C compiler: /nxb-bin/usr/bin/cc -- 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_11d00/fast"
-- Detecting C compile features - failed
-- Check for working CXX compiler: /nxb-bin/usr/bin/c++
-- Check for working CXX compiler: /nxb-bin/usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Check for working C compiler: /nxb-bin/usr/bin/cc -- works
-- Detecting C compile features
-- Detecting C compile features - done
-- Could NOT find SWIG (missing:  SWIG_EXECUTABLE SWIG_DIR) 
-- Looking for BZ2_bzCompressInit in /usr/lib/libbz2.so
-- Looking for BZ2_bzCompressInit in /usr/lib/libbz2.so - found
-- Looking for gzopen in /usr/lib/libz.so
-- Looking for gzopen in /usr/lib/libz.so - found
-- Looking for include file check.h
-- Looking for include file check.h - not found
-- Looking for include file expat.h
-- Looking for include file expat.h - not found
-- Looking for include file errno.h
CMake Error: Generator: execution of make failed. Make command was: "/usr/bin/make" "cmTC_f9b08/fast"
-- Looking for include file errno.h - not found
-- Looking for include file ieeefp.h
-- Looking for include file ieeefp.h - found
-- Looking for include file math.h
-- Looking for include file math.h - found
-- Looking for include file sys/types.h
-- Looking for include file sys/types.h - found
-- Looking for include file float.h
-- Looking for include file float.h - found
-- Check if the system is big endian
-- Searching 16 bit integer
-- Looking for stdint.h
-- Looking for stdint.h - found
-- Looking for stddef.h
-- Looking for stddef.h - found
-- Check size of unsigned short
-- Check size of unsigned short - done
-- Using unsigned short
-- Check if the system is big endian - little endian
-- Looking for sqrt in m
CMake Error: Generator: execution of make failed. Make command was: "/usr/bin/make" "cmTC_df1f7/fast"
-- Looking for sqrt in m - not found
-- 
----------------------------------------------------------------------
libSBML version 5.13.0
----------------------------------------------------------------------

   More information and the latest version are available online at
   http://sbml.org/Software/libSBML

   Please report problems using the issue tracker at
   http://sbml.org/Software/libsbml/issue-tracker

   To contact the developers directly, email libsbml-team at caltech.edu

   Configured on host 'head-armv6-default-job-20'
     host type                       = FreeBSD
     host operating system           = FreeBSD 11.0-CURRENT
     host CPU architecture           = armv6

   General build flags:
     CC                              = /nxb-bin/usr/bin/cc
     CXX                             = /nxb-bin/usr/bin/c++
     CPPFLAGS                        =  -DLINUX
     CFLAGS                          = -O2 -pipe -mfloat-abi=softfp  -I/usr/include -fno-strict-aliasing -fno-strict-aliasing -fPIC
     CXXFLAGS                        = -O2 -pipe -mfloat-abi=softfp -I/usr/include -fno-strict-aliasing -fno-strict-aliasing -fPIC
     LDFLAGS                         =  -L/usr/lib

   XML parser library configuration:
     XML library                     = libxml2
     CPPFLAGS for XML                = -I/usr/local/include/libxml2
     LIBS for XML                    = /usr/local/lib/libxml2.so

   Other libSBML configuration settings:
     Installation $prefix            = /usr/local
--      Value of $LD_LIBRARY_PATH       = 
--      Using SWIG                      = SWIG_EXECUTABLE-NOTFOUND (Version )
--      Using C++ namespace ('libsbml') = no
-- 
--      Build examples                  = no
-- 
--      Use Legacy Math                 = no
-- 
--    Support for SBML Level 3 Packages: 
--      SBML 'layout' package  = OFF
-- 

-- Other potentially important settings:
--   Compression support is enabled for .zip and .gz files
--   Compression support is enabled for .bz2 files
-- 
----------------------------------------------------------------------
-- Configuring incomplete, errors occurred!
See also "/wrkdirs/usr/ports/biology/libsbml/work/.build/CMakeFiles/CMakeOutput.log".
See also "/wrkdirs/usr/ports/biology/libsbml/work/.build/CMakeFiles/CMakeError.log".
*** Error code 1

Stop.
make: stopped in /usr/ports/biology/libsbml