[package - head-armv6-default][biology/seqtools] Failed for seqtools-4.39.3 in configure

Fri Dec 11 13:50:53 UTC 2015

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:     pi at FreeBSD.org
Last committer: pi at FreeBSD.org
Ident:          $FreeBSD: head/biology/seqtools/Makefile 403064 2015-12-05 13:20:21Z pi $
Log URL:        http://beefy8.nyi.freebsd.org/data/head-armv6-default/p403218_s291949/logs/seqtools-4.39.3.log
Build URL:      http://beefy8.nyi.freebsd.org/build.html?mastername=head-armv6-default&build=p403218_s291949
Log:

====>> Building biology/seqtools
build started at Fri Dec 11 13:42:56 UTC 2015
port directory: /usr/ports/biology/seqtools
building for: FreeBSD head-armv6-default-job-24 11.0-CURRENT FreeBSD 11.0-CURRENT r291949 arm
maintained by: pi at FreeBSD.org
Makefile ident:      $FreeBSD: head/biology/seqtools/Makefile 403064 2015-12-05 13:20:21Z pi $
Poudriere version: 3.1.10
Host OSVERSION: 1100085
Jail OSVERSION: 1100091

!!! Jail is newer than host. (Jail: 1100091, Host: 1100085) !!!
!!! 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=1100091
UNAME_v=FreeBSD 11.0-CURRENT r291949
UNAME_r=11.0-CURRENT
BLOCKSIZE=K
MAIL=/var/mail/root
STATUS=1
SAVED_TERM=screen
QEMU_EMULATING=1
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=seqtools-4.39.3
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=3.1.10
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 seqtools-4.39.3:
     DOCS=on: Build and/or install documentation
===> Use 'make config' to modify these settings
---End OPTIONS List---

--CONFIGURE_ARGS--
--prefix=/usr/local ${_LATE_CONFIGURE_ARGS}
--End CONFIGURE_ARGS--

--CONFIGURE_ENV--
PKG_CONFIG=pkgconf XDG_DATA_HOME=/wrkdirs/usr/ports/biology/seqtools/work  XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/seqtools/work  HOME=/wrkdirs/usr/ports/biology/seqtools/work TMPDIR="/tmp" SHELL=/bin/sh CONFIG_SHELL=/bin/sh 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" CONFIG_SITE=/usr/ports/Templates/config.site lt_cv_sys_max_cmd_len=262144
--End CONFIGURE_ENV--

--MAKE_ENV--
XDG_DATA_HOME=/wrkdirs/usr/ports/biology/seqtools/work  XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/seqtools/work  HOME=/wrkdirs/usr/ports/biology/seqtools/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  -I/usr/local/include -Wl,-rpath=/usr/local/lib/gcc48 -fno-strict-aliasing"  CPP="cpp48" CPPFLAGS=""  LDFLAGS=" -L/usr/local/lib -lexecinfo -lcurl -lsqlite3 -lm -Wl,-rpath=/usr/local/lib/gcc48 -L/usr/local/lib/gcc48" LIBS=""  CXX="g++48" CXXFLAGS="-O2 -pipe -mfloat-abi=softfp -I/usr/local/include 
 -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--
OSREL=11.0
PREFIX=%D
LOCALBASE=/usr/local
RESETPREFIX=/usr/local
PORTDOCS=""
PORTEXAMPLES=""
LIB32DIR=lib
GTK2_VERSION="2.10.0"
GTK3_VERSION="3.0.0"
DOCSDIR="share/doc/seqtools"
EXAMPLESDIR="share/examples/seqtools"
DATADIR="share/seqtools"
WWWDIR="www/seqtools"
ETCDIR="etc/seqtools"
--End PLIST_SUB--

--SUB_LIST--
PREFIX=/usr/local
LOCALBASE=/usr/local
DATADIR=/usr/local/share/seqtools
DOCSDIR=/usr/local/share/doc/seqtools
EXAMPLESDIR=/usr/local/share/examples/seqtools
WWWDIR=/usr/local/www/seqtools
ETCDIR=/usr/local/etc/seqtools
--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
RANLIB=/nxb-bin/usr/bin/ranlib
YACC=/nxb-bin/usr/bin/yacc
<snip>
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fc-cache: succeeded
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[head-armv6-default-job-24] |   | `-- Installing libXt-1.1.5,1...
[head-armv6-default-job-24] |   |   `-- Installing libSM-1.2.2_3,1...
[head-armv6-default-job-24] |   |   | `-- Installing libICE-1.0.9_1,1...
[head-armv6-default-job-24] |   |   | `-- Extracting libICE-1.0.9_1,1: .......... done
[head-armv6-default-job-24] |   |   `-- Extracting libSM-1.2.2_3,1: .......... done
[head-armv6-default-job-24] |   | `-- Extracting libXt-1.1.5,1: .......... done
[head-armv6-default-job-24] |   | `-- Installing tiff-4.0.6...
[head-armv6-default-job-24] |   |   `-- Installing jbigkit-2.1_1...
[head-armv6-default-job-24] |   |   `-- Extracting jbigkit-2.1_1: .......... done
[head-armv6-default-job-24] |   | `-- Extracting tiff-4.0.6: .......... done
[head-armv6-default-job-24] |   `-- Extracting gdk-pixbuf2-2.32.1: .......... done
[head-armv6-default-job-24] |   `-- Installing shared-mime-info-1.4...
[head-armv6-default-job-24] |   `-- Extracting shared-mime-info-1.4: .......... done
[head-armv6-default-job-24] `-- Extracting gtk-update-icon-cache-2.24.28: .... done
[head-armv6-default-job-24] `-- Installing python-2.7_2,2...
[head-armv6-default-job-24] |   `-- Installing python2-2_3...
[head-armv6-default-job-24] |   `-- Extracting python2-2_3: ...... done
[head-armv6-default-job-24] `-- Extracting python-2.7_2,2: ..... done
[head-armv6-default-job-24] Extracting gtk2-2.24.28_1: .......... done
Message from trousers-tddl-0.3.10_7:
To run tcsd automatically, add the following line to /etc/rc.conf

tcsd_enable="YES"

You might want to edit /usr/local/etc/tcsd.conf to reflect your setup.

To use TPM, add your_account to '_tss' group like following:

# pw groupadd _tss -m your_account
Message from dejavu-2.35:
Make sure that the freetype module is loaded.  If it is not, add the following
line to the "Modules" section of your X Windows configuration file:

	Load "freetype"

Add the following line to the "Files" section of X Windows configuration file:

	FontPath "/usr/local/share/fonts/dejavu/"

Note: your X Windows configuration file is typically /etc/X11/XF86Config
if you are using XFree86, and /etc/X11/xorg.conf if you are using X.Org.
===>   seqtools-4.39.3 depends on shared library: libgtk-x11-2.0.so - found (/usr/local/lib/libgtk-x11-2.0.so)
===>   Returning to build of seqtools-4.39.3
===>   seqtools-4.39.3 depends on shared library: libpango-1.0.so - found (/usr/local/lib/libpango-1.0.so)
===========================================================================
=======================<phase: configure      >============================
===>  Configuring for seqtools-4.39.3
configure: loading site script /usr/ports/Templates/config.site
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... (cached) /bin/mkdir -p
checking for gawk... (cached) /usr/bin/awk
checking whether make sets $(MAKE)... yes
checking whether the C++ compiler works... no
configure: error: in `/wrkdirs/usr/ports/biology/seqtools/work/seqtools-4.39.3':
configure: error: C++ compiler cannot create executables
See `config.log' for more details.
===>  Script "configure" failed unexpectedly.
Please report the problem to pi at FreeBSD.org [maintainer] and attach the
"/wrkdirs/usr/ports/biology/seqtools/work/seqtools-4.39.3/config.log" including
the output of the failure of your make command. Also, it might be a good idea
to provide an overview of all packages installed on your system (e.g. a
/usr/local/sbin/pkg-static info -g -Ea).
*** Error code 1

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