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Date:      Sat, 4 Mar 2017 02:08:52 GMT
From:      pkg-fallout@FreeBSD.org
To:        pkg-fallout@FreeBSD.org
Subject:   [package - 110mips-quarterly][biology/libsbml] Failed for libsbml-5.13.0 in configure
Message-ID:  <201703040208.v2428qS4030527@beefy14.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:     ports@FreeBSD.org
Last committer: mat@FreeBSD.org
Ident:          $FreeBSD: branches/2017Q1/biology/libsbml/Makefile 425174 2016-11-02 22:45:14Z mat $
Log URL:        http://beefy14.nyi.freebsd.org/data/110mips-quarterly/435355/logs/libsbml-5.13.0.log
Build URL:      http://beefy14.nyi.freebsd.org/build.html?mastername=110mips-quarterly&build=435355
Log:

====>> Building biology/libsbml
build started at Sat Mar  4 02:07:36 UTC 2017
port directory: /usr/ports/biology/libsbml
building for: FreeBSD 110mips-quarterly-job-22 11.0-RELEASE-p8 FreeBSD 11.0-RELEASE-p8 r314125 mips
maintained by: ports@FreeBSD.org
Makefile ident:      $FreeBSD: branches/2017Q1/biology/libsbml/Makefile 425174 2016-11-02 22:45:14Z mat $
Poudriere version: 3.1.14
Host OSVERSION: 1200020
Jail OSVERSION: 1100122
Job Id: 22

---Begin Environment---
SHELL=/bin/csh
UNAME_p=mips
UNAME_m=mips
ABI_FILE=/usr/lib/crt1.o
OSVERSION=1100122
UNAME_v=FreeBSD 11.0-RELEASE-p8 r314125
UNAME_r=11.0-RELEASE-p8
BLOCKSIZE=K
MAIL=/var/mail/root
STATUS=1
SAVED_TERM=
MASTERMNT=/usr/local/poudriere/data/.m/110mips-quarterly/ref
QEMU_EMULATING=1
PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin
POUDRIERE_BUILD_TYPE=bulk
PKGNAME=libsbml-5.13.0
OLDPWD=/
PWD=/usr/local/poudriere/data/.m/110mips-quarterly/ref/.p/pool
MASTERNAME=110mips-quarterly
SCRIPTPREFIX=/usr/local/share/poudriere
USER=root
HOME=/root
POUDRIERE_VERSION=3.1.14
SCRIPTPATH=/usr/local/share/poudriere/bulk.sh
LIBEXECPREFIX=/usr/local/libexec/poudriere
LOCALBASE=/usr/local
PACKAGE_BUILDING=yes
---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 MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES PREFIX=/usr/local  LOCALBASE=/usr/local  LIBDIR="/usr/lib"  CC="/nxb-bin/usr/bin/cc" CFLAGS="-O2 -pipe -G0  -I/usr/include -DLIBICONV_PLUG -fno-strict-aliasing"  CPP="/nxb-bin/usr/bin/cpp" CPPFLAGS="-DLIBICONV_PLUG"  LDFLAGS=" -L/usr/lib" LIBS=""  CXX="/nxb-bin/usr/bin/c++" CXXFLAGS="-O2 -pipe -G0 -I/usr/include -DLIBICONV_PLUG -fno-strict-aliasing  -DLIBICONV_PLUG"  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---
.sinclude "/etc/make.nxb.conf"
USE_PACKAGE_DEPENDS=yes
BATCH=yes
WRKDIRPREFIX=/wrkdirs
PORTSDIR=/usr/ports
PACKAGES=/packages
DISTDIR=/distfiles
MACHINE=mips
MACHINE_ARCH=mips
ARCH=${MACHINE_ARCH}
#### /usr/local/etc/poudriere.d/make.conf ####
# XXX: We really need this but cannot use it while 'make checksum' does not
# try the next mirror on checksum failure.  It currently retries the same
# failed mirror and then fails rather then trying another.  It *does*
# try the next if the size is mismatched though.
#MASTER_SITE_FREEBSD=yes
# Build ALLOW_MAKE_JOBS_PACKAGES with 2 jobs
MAKE_JOBS_NUMBER=2
#### /usr/ports/Mk/Scripts/ports_env.sh ####
ARCH=mips
CONFIGURE_MAX_CMD_LEN=262144
OPSYS=FreeBSD
OSREL=11.0
OSVERSION=1100122
PYTHONBASE=/usr/local
UID=0
_JAVA_OS_LIST_REGEXP=native\|linux
_JAVA_VENDOR_LIST_REGEXP=openjdk\|oracle\|sun
_JAVA_VERSION_LIST_REGEXP=1.6\|1.7\|1.8\|1.6+\|1.7+\|1.8+
_OSRELEASE=11.0-RELEASE-p8
#### Misc Poudriere ####
GID=0
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---
--Resource limits--
cpu time               (seconds, -t)  unlimited
file size           (512-blocks, -f)  unlimited
data seg size           (kbytes, -d)  131072
stack size              (kbytes, -s)  8192
core file size      (512-blocks, -c)  unlimited
max memory size         (kbytes, -m)  unlimited
locked memory           (kbytes, -l)  unlimited
max user processes              (-u)  89999
open files                      (-n)  1024
virtual mem size        (kbytes, -v)  unlimited
swap limit              (kbytes, -w)  unlimited
socket buffer size       (bytes, -b)  unlimited
pseudo-terminals                (-p)  unlimited
kqueues                         (-k)  unlimited
umtx shared locks               (-o)  unlimited
--End resource limits--
=======================<phase: check-sanity   >============================
===>   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
===========================================================================
=======================<phase: pkg-depends    >============================
===>   libsbml-5.13.0 depends on file: /usr/local/sbin/pkg - not found
===>   Installing existing package /packages/All/pkg-1.9.4_1.txz
[110mips-quarterly-job-22] Installing pkg-1.9.4_1...
[110mips-quarterly-job-22] Extracting pkg-1.9.4_1: .......... done
<snip>
===========================================================================
=======================<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-3.7.1.txz
[110mips-quarterly-job-22] Installing cmake-3.7.1...
[110mips-quarterly-job-22] `-- Installing expat-2.2.0_1...
[110mips-quarterly-job-22] `-- Extracting expat-2.2.0_1: .......... done
[110mips-quarterly-job-22] `-- Installing cmake-modules-3.7.1...
[110mips-quarterly-job-22] `-- Extracting cmake-modules-3.7.1: .......... done
[110mips-quarterly-job-22] `-- Installing curl-7.53.0...
[110mips-quarterly-job-22] |   `-- Installing libnghttp2-1.18.0...
[110mips-quarterly-job-22] |   `-- Extracting libnghttp2-1.18.0: .......... done
[110mips-quarterly-job-22] |   `-- Installing ca_root_nss-3.29.1...
[110mips-quarterly-job-22] |   `-- Extracting ca_root_nss-3.29.1: ........ done
[110mips-quarterly-job-22] `-- Extracting curl-7.53.0: .......... done
[110mips-quarterly-job-22] `-- Installing libarchive-3.2.2,1...
[110mips-quarterly-job-22] |   `-- Installing liblz4-131...
[110mips-quarterly-job-22] |   `-- Extracting liblz4-131: .......... done
[110mips-quarterly-job-22] |   `-- Installing lzo2-2.09...
[110mips-quarterly-job-22] |   `-- Extracting lzo2-2.09: .......... done
[110mips-quarterly-job-22] `-- Extracting libarchive-3.2.2,1: .......... done
[110mips-quarterly-job-22] `-- Installing jsoncpp-1.8.0_1...
[110mips-quarterly-job-22] `-- Extracting jsoncpp-1.8.0_1: .......... done
[110mips-quarterly-job-22] `-- Installing libuv-1.10.1...
[110mips-quarterly-job-22] `-- Extracting libuv-1.10.1: .......... done
[110mips-quarterly-job-22] Extracting cmake-3.7.1: .......... done
Message from ca_root_nss-3.29.1:
********************************* 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/libxml2-2.9.4.txz
[110mips-quarterly-job-22] Installing libxml2-2.9.4...
[110mips-quarterly-job-22] Extracting libxml2-2.9.4: .......... 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 GNU 4.2.1
-- The CXX compiler identification is GNU 4.2.1
-- 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
-- Detecting C compile features - done
-- 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
-- Looking for include file errno.h - found
-- Looking for include file ieeefp.h
CMake Error: Generator: execution of make failed. Make command was: "/usr/bin/make" "cmTC_c8d92/fast"
-- Looking for include file ieeefp.h - not found
-- Looking for include file math.h
CMake Error: Generator: execution of make failed. Make command was: "/usr/bin/make" "cmTC_0da20/fast"
-- Looking for include file math.h - not 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 - big endian
-- Looking for sqrt in m
CMake Error: Generator: execution of make failed. Make command was: "/usr/bin/make" "cmTC_223f9/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@caltech.edu

   Configured on host '110mips-quarterly-job-22'
     host type                       = FreeBSD
     host operating system           = FreeBSD 11.0-RELEASE-p8
     host CPU architecture           = mips

   General build flags:
     CC                              = /nxb-bin/usr/bin/cc
     CXX                             = /nxb-bin/usr/bin/c++
     CPPFLAGS                        =  -DLINUX
     CFLAGS                          = -O2 -pipe -G0  -I/usr/include -DLIBICONV_PLUG -fno-strict-aliasing -fno-strict-aliasing -fPIC
     CXXFLAGS                        = -O2 -pipe -G0 -I/usr/include -DLIBICONV_PLUG -fno-strict-aliasing  -DLIBICONV_PLUG -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



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