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Date:      Fri, 15 Feb 2019 14:15:07 GMT
From:      pkg-fallout@FreeBSD.org
To:        pkg-fallout@FreeBSD.org
Subject:   [package - 120powerpc64-quarterly][science/coot] Failed for coot-0.8.9.1_2 in configure
Message-ID:  <201902151415.x1FEF79V093960@pylon.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:     yuri@FreeBSD.org
Last committer: gerald@FreeBSD.org
Ident:          $FreeBSD: branches/2019Q1/science/coot/Makefile 487272 2018-12-12 01:35:33Z gerald $
Log URL:        http://pylon.nyi.freebsd.org/data/120powerpc64-quarterly/492798/logs/coot-0.8.9.1_2.log
Build URL:      http://pylon.nyi.freebsd.org/build.html?mastername=120powerpc64-quarterly&build=492798
Log:

=>> Building science/coot
build started at Fri Feb 15 14:12:47 UTC 2019
port directory: /usr/ports/science/coot
package name: coot-0.8.9.1_2
building for: FreeBSD 120powerpc64-quarterly-job-03 12.0-RELEASE-p3 FreeBSD 12.0-RELEASE-p3 1200086 powerpc
maintained by: yuri@FreeBSD.org
Makefile ident:      $FreeBSD: branches/2019Q1/science/coot/Makefile 487272 2018-12-12 01:35:33Z gerald $
Poudriere version: 3.2.8-1-g2a843cca
Host OSVERSION: 1300012
Jail OSVERSION: 1200086
Job Id: 03

---Begin Environment---
SHELL=/bin/csh
OSVERSION=1200086
UNAME_v=FreeBSD 12.0-RELEASE-p3 1200086
UNAME_r=12.0-RELEASE-p3
BLOCKSIZE=K
MAIL=/var/mail/root
STATUS=1
HOME=/root
PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin
LOCALBASE=/usr/local
USER=root
LIBEXECPREFIX=/usr/local/libexec/poudriere
POUDRIERE_VERSION=3.2.8-1-g2a843cca
MASTERMNT=/usr/local/poudriere/data/.m/120powerpc64-quarterly/ref
POUDRIERE_BUILD_TYPE=bulk
PACKAGE_BUILDING=yes
SAVED_TERM=vt100
PWD=/usr/local/poudriere/data/.m/120powerpc64-quarterly/ref/.p/pool
P_PORTS_FEATURES=FLAVORS SELECTED_OPTIONS
MASTERNAME=120powerpc64-quarterly
SCRIPTPREFIX=/usr/local/share/poudriere
OLDPWD=/usr/local/poudriere/data/.m/120powerpc64-quarterly/ref/.p
SCRIPTPATH=/usr/local/share/poudriere/bulk.sh
POUDRIEREPATH=/usr/local/bin/poudriere
---End Environment---

---Begin Poudriere Port Flags/Env---
PORT_FLAGS=
PKGENV=
FLAVOR=
DEPENDS_ARGS=
MAKE_ARGS=
---End Poudriere Port Flags/Env---

---Begin OPTIONS List---
---End OPTIONS List---

--MAINTAINER--
yuri@FreeBSD.org
--End MAINTAINER--

--CONFIGURE_ARGS--
--enable-shared --disable-static --x-libraries=/usr/local/lib --x-includes=/usr/local/include --prefix=/usr/local ${_LATE_CONFIGURE_ARGS}
--End CONFIGURE_ARGS--

--CONFIGURE_ENV--
F77="gfortran8" FC="gfortran8" FFLAGS="-O -Wl,-rpath=/usr/local/lib/gcc8" FCFLAGS="-Wl,-rpath=/usr/local/lib/gcc8" MAKE=gmake PKG_CONFIG=pkgconf PYTHON="/usr/local/bin/python2.7" XDG_DATA_HOME=/wrkdirs/usr/ports/science/coot/work  XDG_CONFIG_HOME=/wrkdirs/usr/ports/science/coot/work  HOME=/wrkdirs/usr/ports/science/coot/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/science/coot/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin 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" CMAKE_PREFIX_PATH="/usr/local" LANG=en_US.UTF-8 LC_ALL=en_US.UTF-8 CONFIG_SITE=/usr/ports/Templates/config.site lt_cv_sys_m
 ax_cmd_len=262144
--End CONFIGURE_ENV--

--MAKE_ENV--
PYTHON=/usr/local/bin/python2.7 F77="gfortran8" FC="gfortran8" FFLAGS="-O -Wl,-rpath=/usr/local/lib/gcc8" FCFLAGS="-Wl,-rpath=/usr/local/lib/gcc8" XDG_DATA_HOME=/wrkdirs/usr/ports/science/coot/work  XDG_CONFIG_HOME=/wrkdirs/usr/ports/science/coot/work  HOME=/wrkdirs/usr/ports/science/coot/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/science/coot/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin NO_PIE=yes MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no 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" LANG=en_US.UTF-8 LC_ALL=en_US.UTF-8 PREFIX=/usr/local  LOCALBASE=/usr/local  CC="cc" CFLAGS="-O2 -pipe  -isystem /
 usr/local/include -fno-strict-aliasing "  CPP="cpp" CPPFLAGS="-isystem /usr/local/include"  LDFLAGS=" -Wl,-rpath=/usr/local/lib/gcc8  -L/usr/local/lib/gcc8 -B/usr/local/bin -L/usr/local/lib " LIBS=""  CXX="c++" CXXFLAGS="-O2 -pipe -isystem /usr/local/include -fno-strict-aliasing  -I/usr/local/include/python2.7 -isystem /usr/local/include "  MANPREFIX="/usr/local" BSD_INSTALL_PROGRAM="install  -s -m 555"  BSD_INSTALL_LIB="install  -s -m 0644"  BSD_INSTALL_SCRIPT="install  -m 555"  BSD_INSTALL_DATA="install  -m 0644"  BSD_INSTALL_MAN="install  -m 444"
--End MAKE_ENV--

--PLIST_SUB--
PYTHON_INCLUDEDIR=include/python2.7  PYTHON_LIBDIR=lib/python2.7  PYTHON_PLATFORM=freebsd12  PYTHON_PYOEXTENSION=pyo  PYTHON_SITELIBDIR=lib/python2.7/site-packages  PYTHON_SUFFIX=27  PYTHON_VER=2.7  PYTHON_VERSION=python2.7 PYTHON2="" PYTHON3="@comment " GTK2_VERSION="2.10.0"  GTK3_VERSION="3.0.0" OSREL=12.0 PREFIX=%D LOCALBASE=/usr/local  RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/coot"  EXAMPLESDIR="share/examples/coot"  DATADIR="share/coot"  WWWDIR="www/coot"  ETCDIR="etc/coot"
--End PLIST_SUB--

--SUB_LIST--
PREFIX=/usr/local LOCALBASE=/usr/local  DATADIR=/usr/local/share/coot DOCSDIR=/usr/local/share/doc/coot EXAMPLESDIR=/usr/local/share/examples/coot  WWWDIR=/usr/local/www/coot ETCDIR=/usr/local/etc/coot
--End SUB_LIST--

---Begin make.conf---
USE_PACKAGE_DEPENDS=yes
BATCH=yes
WRKDIRPREFIX=/wrkdirs
PORTSDIR=/usr/ports
PACKAGES=/packages
DISTDIR=/distfiles
PACKAGE_BUILDING=yes
PACKAGE_BUILDING_FLAVORS=yes
#### /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

# stable/10 includes src.conf too late but make.conf is in sys.mk
.if ${.CURDIR:M/poudriere/jails/10*/usr/src/usr.bin/xlint*}
# Disable build of llib now that head no longer has lint(1)
LINT=	true
.endif
#### /usr/ports/Mk/Scripts/ports_env.sh ####
_CCVERSION_921dbbb2=cc (GCC) 4.2.1 20070831 patched [FreeBSD] Copyright (C) 2007 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
_ALTCCVERSION_921dbbb2=none
_CXXINTERNAL_acaad9ca=Using built-in specs. Target: powerpc64-undermydesk-freebsd Configured with: FreeBSD/powerpc64 system compiler Thread model: posix gcc version 4.2.1 20070831 patched [FreeBSD] "/usr/bin/ld" "--eh-frame-hdr" "-Qy" "-melf64ppc_fbsd" "--enable-new-dtags" "-dynamic-linker" "/libexec/ld-elf.so.1" "/usr/lib/crt1.o" "/usr/lib/crti.o" "/usr/lib/crtbegin.o" "-L/usr/lib" "-L/usr/lib" "/dev/null" "-lstdc++" "-lm" "-lgcc_s" "-lgcc" "-lc" "-lgcc_s" "-lgcc" "/usr/lib/crtsavres.o" "/usr/lib/crtend.o" "/usr/lib/crtn.o"
CC_OUTPUT_921dbbb2_58173849=yes
CC_OUTPUT_921dbbb2_9bdba57c=yes
CC_OUTPUT_921dbbb2_6a4fe7f5=cc1: error: unrecognized command line option "-std=c11"
CC_OUTPUT_921dbbb2_6bcac02b=yes
CC_OUTPUT_921dbbb2_67d20829=yes
CC_OUTPUT_921dbbb2_bfa62e83=cc1: error: unrecognized command line option "-std=gnu11"
CC_OUTPUT_921dbbb2_f0b4d593=yes
CC_OUTPUT_921dbbb2_308abb44=cc1plus: error: unrecognized command line option "-std=c++0x"
CC_OUTPUT_921dbbb2_f00456e5=cc1plus: error: unrecognized command line option "-std=c++11"
CC_OUTPUT_921dbbb2_65ad290d=cc1plus: error: unrecognized command line option "-std=c++14"
CC_OUTPUT_921dbbb2_f2776b26=cc1plus: error: unrecognized command line option "-std=c++17"
CC_OUTPUT_921dbbb2_b2657cc3=yes
CC_OUTPUT_921dbbb2_380987f7=cc1plus: error: unrecognized command line option "-std=gnu++11"
CC_OUTPUT_921dbbb2_160933ec=cc1plus: error: unrecognized command line option "-std=gnu++14"
CC_OUTPUT_921dbbb2_fb62803b=cc1plus: error: unrecognized command line option "-std=gnu++17"
_OBJC_CCVERSION_921dbbb2=cc (GCC) 4.2.1 20070831 patched [FreeBSD] Copyright (C) 2007 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
_OBJC_ALTCCVERSION_921dbbb2=none
ARCH=powerpc64
OPSYS=FreeBSD
_OSRELEASE=12.0-RELEASE-p3
OSREL=12.0
OSVERSION=1200086
PYTHONBASE=/usr/local
CONFIGURE_MAX_CMD_LEN=262144
HAVE_PORTS_ENV=1
#### Misc Poudriere ####
GID=0
UID=0
DISABLE_MAKE_JOBS=poudriere
---End make.conf---
--Resource limits--
cpu time               (seconds, -t)  unlimited
file size           (512-blocks, -f)  unlimited
data seg size           (kbytes, -d)  33554432
stack size              (kbytes, -s)  524288
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   >============================
===>  License LGPL3 accepted by the user
===========================================================================
=======================<phase: pkg-depends    >============================
===>   coot-0.8.9.1_2 depends on file: /usr/local/sbin/pkg - not found
===>   Installing existing package /packages/All/pkg-1.10.5_5.txz
[120powerpc64-quarterly-job-03] Installing pkg-1.10.5_5...
[120powerpc64-quarterly-job-03] Extracting pkg-1.10.5_5: .......... done
===>   coot-0.8.9.1_2 depends on file: /usr/local/sbin/pkg - found
===>   Returning to build of coot-0.8.9.1_2
===========================================================================
=======================<phase: fetch-depends  >============================
===========================================================================
=======================<phase: fetch          >============================
===>  License LGPL3 accepted by the user
=> coot-0.8.9.1.tar.gz doesn't seem to exist in /portdistfiles/coot.
=> Attempting to fetch https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/source/releases/coot-0.8.9.1.tar.gz
coot-0.8.9.1.tar.gz                                     18 MB 3994 kBps    05s
=> refmac-monomer-library.tar.gz doesn't seem to exist in /portdistfiles/coot.
=> Attempting to fetch https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/dependencies/refmac-monomer-library.tar.gz
refmac-monomer-library.tar.gz                           35 MB  977 kBps    38s
=> reference-structures.tar.gz doesn't seem to exist in /portdistfiles/coot.
=> Attempting to fetch https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/dependencies/reference-structures.tar.gz
reference-structures.tar.gz                           6571 kB 2266 kBps    03s
===> Fetching all distfiles required by coot-0.8.9.1_2 for building
===========================================================================
=======================<phase: checksum       >============================
===>  License LGPL3 accepted by the user
===> Fetching all distfiles required by coot-0.8.9.1_2 for building
=> SHA256 Checksum OK for coot/coot-0.8.9.1.tar.gz.
=> SHA256 Checksum OK for coot/refmac-monomer-library.tar.gz.
=> SHA256 Checksum OK for coot/reference-structures.tar.gz.
===========================================================================
=======================<phase: extract-depends>============================
===========================================================================
=======================<phase: extract        >============================
===>  License LGPL3 accepted by the user
===> Fetching all distfiles required by coot-0.8.9.1_2 for building
===>  Extracting for coot-0.8.9.1_2
=> SHA256 Checksum OK for coot/coot-0.8.9.1.tar.gz.
=> SHA256 Checksum OK for coot/refmac-monomer-library.tar.gz.
=> SHA256 Checksum OK for coot/reference-structures.tar.gz.
===========================================================================
=======================<phase: patch-depends  >============================
===========================================================================
=======================<phase: patch          >============================
===>  Patching for coot-0.8.9.1_2
===>  Applying FreeBSD patches for coot-0.8.9.1_2
===========================================================================
=======================<phase: build-depends  >============================
===>   coot-0.8.9.1_2 depends on executable: update-desktop-database - not found
<snip>
===>   coot-0.8.9.1_2 depends on shared library: libart_lgpl_2.so - found (/usr/local/lib/libart_lgpl_2.so)
===>   Returning to build of coot-0.8.9.1_2
===>   coot-0.8.9.1_2 depends on shared library: libglade-2.0.so - not found
===>   Installing existing package /packages/All/libglade2-2.6.4_9.txz
[120powerpc64-quarterly-job-03] Installing libglade2-2.6.4_9...
[120powerpc64-quarterly-job-03] `-- Installing xmlcatmgr-2.2_2...
[120powerpc64-quarterly-job-03] `-- Extracting xmlcatmgr-2.2_2: ......... done
 + Creating /usr/local/share/sgml/catalog
 + Registering CATALOG catalog.ports (SGML)
 + Creating /usr/local/share/sgml/catalog.ports
 + Creating /usr/local/share/xml/catalog
 + Registering nextCatalog catalog.ports (XML)
 + Creating /usr/local/share/xml/catalog.ports
[120powerpc64-quarterly-job-03] Extracting libglade2-2.6.4_9: .......... done
Message from xmlcatmgr-2.2_2:

The following catalogs are installed:

 1) /usr/local/share/sgml/catalog

   The top level catalog for SGML stuff.  It is not changed
   by any ports/packages except textproc/xmlcatmgr.

 2) /usr/local/share/sgml/catalog.ports

   This catalog is for handling SGML stuff installed under
   /usr/local/share/sgml.  It is changed by ports/packages.

 3) /usr/local/share/xml/catalog

   The top level catalog for XML stuff.  It is not changed
   by any ports/packages except textproc/xmlcatmgr.

 4) /usr/local/share/xml/catalog.ports

   This catalog is for handling XML stuff installed under
   /usr/local/share/xml.  It is changed by ports/packages.
===>   coot-0.8.9.1_2 depends on shared library: libglade-2.0.so - found (/usr/local/lib/libglade-2.0.so)
===>   Returning to build of coot-0.8.9.1_2
===>   coot-0.8.9.1_2 depends on shared library: libgnomecanvas-2.so - not found
===>   Installing existing package /packages/All/libgnomecanvas-2.30.3_4.txz
[120powerpc64-quarterly-job-03] Installing libgnomecanvas-2.30.3_4...
[120powerpc64-quarterly-job-03] Extracting libgnomecanvas-2.30.3_4: .......... done
===>   coot-0.8.9.1_2 depends on shared library: libgnomecanvas-2.so - found (/usr/local/lib/libgnomecanvas-2.so)
===>   Returning to build of coot-0.8.9.1_2
===>   coot-0.8.9.1_2 depends on shared library: libxml2.so - found (/usr/local/lib/libxml2.so)
===>   coot-0.8.9.1_2 depends on shared library: libpango-1.0.so - found (/usr/local/lib/libpango-1.0.so)
===>   coot-0.8.9.1_2 depends on shared library: libpangox-1.0.so - found (/usr/local/lib/libpangox-1.0.so)
===>   coot-0.8.9.1_2 depends on shared library: libGL.so - found (/usr/local/lib/libGL.so)
===>   coot-0.8.9.1_2 depends on shared library: libGLU.so - found (/usr/local/lib/libGLU.so)
===>   coot-0.8.9.1_2 depends on shared library: libglut.so - not found
===>   Installing existing package /packages/All/freeglut-3.0.0_2.txz
[120powerpc64-quarterly-job-03] Installing freeglut-3.0.0_2...
[120powerpc64-quarterly-job-03] Extracting freeglut-3.0.0_2: .......... done
Message from freeglut-3.0.0_2:

Joystick support is untested and it is unknown if it works.

Do not hesitate to contact x11@FreeBSD.org if this causes issues.
===>   coot-0.8.9.1_2 depends on shared library: libglut.so - found (/usr/local/lib/libglut.so)
===>   Returning to build of coot-0.8.9.1_2
===========================================================================
=======================<phase: configure      >============================
===>  Configuring for coot-0.8.9.1_2
===>   FreeBSD 10 autotools fix applied to /wrkdirs/usr/ports/science/coot/work/coot-0.8.9.1/macros/libtool.m4
===>   FreeBSD 10 autotools fix applied to /wrkdirs/usr/ports/science/coot/work/coot-0.8.9.1/configure
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 gmake sets $(MAKE)... yes
checking for style of include used by gmake... GNU
checking for gcc... cc
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables... 
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether cc accepts -g... yes
checking for cc option to accept ISO C89... none needed
checking dependency style of cc... gcc3
checking for library containing strerror... none required
checking for gcc... (cached) cc
checking whether we are using the GNU C compiler... (cached) yes
checking whether cc accepts -g... (cached) yes
checking for cc option to accept ISO C89... (cached) none needed
checking dependency style of cc... (cached) gcc3
checking how to run the C preprocessor... cpp
checking for grep that handles long lines and -e... (cached) /usr/bin/grep
checking for egrep... (cached) /usr/bin/egrep
checking for ANSI C header files... (cached) yes
checking whether we are using the GNU C++ compiler... yes
checking whether c++ accepts -g... yes
checking dependency style of c++... gcc3
checking build system type... powerpc64-portbld-freebsd12.0
checking host system type... powerpc64-portbld-freebsd12.0
checking for a sed that does not truncate output... (cached) /usr/bin/sed
checking for fgrep... (cached) /usr/bin/fgrep
checking for ld used by cc... /usr/local/bin/ld
checking if the linker (/usr/local/bin/ld) is GNU ld... yes
checking for BSD- or MS-compatible name lister (nm)... /usr/local/bin/nm
checking the name lister (/usr/local/bin/nm) interface... BSD nm
checking whether ln -s works... yes
checking the maximum length of command line arguments... (cached) 262144
checking whether the shell understands some XSI constructs... yes
checking whether the shell understands "+="... no
checking for /usr/local/bin/ld option to reload object files... -r
checking for objdump... /usr/local/bin/objdump
checking how to recognize dependent libraries... pass_all
checking for ar... /usr/local/bin/ar
checking for strip... strip
checking for ranlib... /usr/local/bin/ranlib
checking command to parse /usr/local/bin/nm output from cc object... ok
checking for sys/types.h... (cached) yes
checking for sys/stat.h... (cached) yes
checking for stdlib.h... (cached) yes
checking for string.h... (cached) yes
checking for memory.h... (cached) yes
checking for strings.h... (cached) yes
checking for inttypes.h... (cached) yes
checking for stdint.h... (cached) yes
checking for unistd.h... (cached) yes
checking for dlfcn.h... (cached) yes
checking whether we are using the GNU C++ compiler... (cached) yes
checking whether c++ accepts -g... (cached) yes
checking dependency style of c++... (cached) gcc3
checking how to run the C++ preprocessor... c++ -E
checking for objdir... .libs
checking if cc supports -fno-rtti -fno-exceptions... no
checking for cc option to produce PIC... -fPIC -DPIC
checking if cc PIC flag -fPIC -DPIC works... yes
checking if cc static flag -static works... yes
checking if cc supports -c -o file.o... yes
checking if cc supports -c -o file.o... (cached) yes
checking whether the cc linker (/usr/local/bin/ld) supports shared libraries... yes
checking whether -lc should be explicitly linked in... no
checking dynamic linker characteristics... freebsd12.0 ld.so
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... no
checking for ld used by c++... /usr/local/bin/ld
checking if the linker (/usr/local/bin/ld) is GNU ld... yes
checking whether the c++ linker (/usr/local/bin/ld) supports shared libraries... yes
checking for c++ option to produce PIC... -fPIC -DPIC
checking if c++ PIC flag -fPIC -DPIC works... yes
checking if c++ static flag -static works... yes
checking if c++ supports -c -o file.o... yes
checking if c++ supports -c -o file.o... (cached) yes
checking whether the c++ linker (/usr/local/bin/ld) supports shared libraries... yes
checking dynamic linker characteristics... freebsd12.0 ld.so
checking how to hardcode library paths into programs... immediate
checking which libtool initialization strategy to adopt... AC-PROG-LIBTOOL
checking what warning flags to pass to the C compiler... -Wall -Wunused
checking what language compliance flags to pass to the C compiler... 
checking what warning flags to pass to the C++ compiler... -Wall -Wno-unused
checking what language compliance flags to pass to the C++ compiler... 
checking sys/stdtypes.h usability... no
checking sys/stdtypes.h presence... no
checking for sys/stdtypes.h... no
checking for OpenMP flag of C compiler... -fopenmp
checking pkg-config is at least version 0.9.0... yes
checking for GLIB... yes
checking if this is MINGW on Windows... no
checking for SQLite3... yes
checking for mmdb2... yes
checking for ssm... yes
no
checking for prefixed single-precision FFTW2 (sfftw.h)... yes
checking for Clipper... yes
Not using guile
checking for gsl-config... /usr/local/bin/gsl-config
checking for GSL - version >= 1.3... yes
checking for GTK... yes
checking for GNOME_CANVAS... yes
checking for pkg-config... /usr/local/bin/pkg-config
checking for GtkGLExt - version >= 1.0.0... no
*** Could not run GtkGLExt test program, checking why...
*** The test program compiled, but did not run. This usually means
*** that the run-time linker is not finding GtkGLExt or finding the wrong
*** version of GtkGLExt. If it is not finding GtkGLExt, you'll need to set your
*** LD_LIBRARY_PATH environment variable, or edit /etc/ld.so.conf to point
*** to the installed location  Also, make sure you have run ldconfig if that
*** is required on your system
***
*** If you have an old version installed, it is best to remove it, although
*** you may also be able to get things to work by modifying LD_LIBRARY_PATH
===>  Script "configure" failed unexpectedly.
Please report the problem to yuri@FreeBSD.org [maintainer] and attach the
"/wrkdirs/usr/ports/science/coot/work/coot-0.8.9.1/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/science/coot



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