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Please investigate the failure and submit a PR to fix
build.

Maintainer:     koz...@hdfgroup.org
Last committer: mar...@freebsd.org
Ident:          $FreeBSD: head/science/hdf5/Makefile 323491 2013-07-22 
18:17:31Z marino $
Log URL:        
http://beefy1.isc.freebsd.org/bulk/head-i386-default/2013-09-19_00h27m24s/logs/hdf5-1.6.9_2.log
Build URL:      
http://beefy1.isc.freebsd.org/bulk/head-i386-default/2013-09-19_00h27m24s
Log:

====>> Building science/hdf5
build started at Thu Sep 19 00:42:22 UTC 2013
port directory: /usr/ports/science/hdf5
building for: FreeBSD head-i386-default-job-03 10.0-CURRENT FreeBSD 
10.0-CURRENT i386
maintained by: koz...@hdfgroup.org
Makefile ident:      $FreeBSD: head/science/hdf5/Makefile 323491 2013-07-22 
18:17:31Z marino $
Poudriere version: 3.1-pre

---Begin Environment---
UNAME_m=i386
UNAME_p=i386
OSVERSION=1000055
UNAME_v=FreeBSD 10.0-CURRENT
UNAME_r=10.0-CURRENT
BLOCKSIZE=K
MAIL=/var/mail/root
STATUS=1
MASTERMNT=/usr/local/poudriere/data/build/head-i386-default/ref
PKG_EXT=txz
tpid=68700
PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/games:/usr/local/sbin:/usr/local/bin:/root/bin
POUDRIERE_BUILD_TYPE=bulk
NBPARALLEL=24
PKGNG=1
PKGNAME=hdf5-1.6.9_2
PKG_DELETE=/usr/local/sbin/pkg delete -y -f
PKG_ADD=/usr/local/sbin/pkg add
PWD=/root
MASTERNAME=head-i386-default
USER=root
HOME=/root
POUDRIERE_VERSION=3.1-pre
SKIPSANITY=1
LOCALBASE=/usr/local
PACKAGE_BUILDING=yes
---End Environment---

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

--CONFIGURE_ARGS--
--disable-debug  --enable-cxx  --enable-instrument  --enable-production  
--enable-strict-format-checks  --enable-threadsafe  --with-pthread=/usr  
--with-ssl=/usr  --with-zlib=/usr --prefix=/usr/local ${_LATE_CONFIGURE_ARGS}
--End CONFIGURE_ARGS--

--CONFIGURE_ENV--
TMPDIR="/tmp" TMPDIR="/tmp" SHELL=/bin/sh CONFIG_SHELL=/bin/sh   
LIBTOOL=/usr/local/bin/libtool  LIBTOOLIZE=/usr/local/bin/libtoolize  
LIBTOOL_LIBEXECDIR=/usr/local/libexec/libtool  
LIBTOOL_SHAREDIR=/usr/local/share/libtool  
LIBTOOL_M4=/usr/local/share/aclocal/libtool.m4  
LTMAIN=/usr/local/share/libtool/config/ltmain.sh 
CONFIG_SITE=/usr/ports/Templates/config.site lt_cv_sys_max_cmd_len=262144
--End CONFIGURE_ENV--

--MAKE_ENV--
TMPDIR="/tmp" TMPDIR="/tmp" SHELL=/bin/sh NO_LINT=YES   
LIBTOOL=/usr/local/bin/libtool  LIBTOOLIZE=/usr/local/bin/libtoolize  
LIBTOOL_LIBEXECDIR=/usr/local/libexec/libtool  
LIBTOOL_SHAREDIR=/usr/local/share/libtool  
LIBTOOL_M4=/usr/local/share/aclocal/libtool.m4  
LTMAIN=/usr/local/share/libtool/config/ltmain.sh 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/hdf5
DOCSDIR=/usr/local/share/doc/hdf5
EXAMPLESDIR=/usr/local/share/examples/hdf5
WWWDIR=/usr/local/www/hdf5
ETCDIR=/usr/local/etc/hdf5
--End SUB_LIST--

---Begin make.conf---
ARCH=i386
MACHINE=i386
MACHINE_ARCH=i386
USE_PACKAGE_DEPENDS=yes
BATCH=yes
WRKDIRPREFIX=/wrkdirs
PACKAGES=/packages
DISTDIR=/distfiles
#### /usr/local/etc/poudriere.d/make.conf ####
WITH_PKGNG=yes
NO_RESTRICTED=yes
DISABLE_MAKE_JOBS=yes
---End make.conf---
===>  Cleaning for hdf5-1.6.9_2
=======================<phase: check-config   >============================
===========================================================================
=======================<phase: pkg-depends    >============================
===>   hdf5-1.6.9_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_2.txz
Installing pkg-1.1.4_2... done
If you are upgrading from the old package format, first run:

  # pkg2ng
===>   Returning to build of hdf5-1.6.9_2
===========================================================================
=======================<phase: fetch-depends  >============================
===========================================================================
=======================<phase: fetch          >============================
===> Fetching all distfiles required by hdf5-1.6.9_2 for building
===========================================================================
=======================<phase: checksum       >============================
===> Fetching all distfiles required by hdf5-1.6.9_2 for building
=> SHA256 Checksum OK for hdf5-1.6.9.tar.gz.
===========================================================================
=======================<phase: extract-depends>============================
===========================================================================
=======================<phase: extract        >============================
===> Fetching all distfiles required by hdf5-1.6.9_2 for building
===>  Extracting for hdf5-1.6.9_2
=> SHA256 Checksum OK for hdf5-1.6.9.tar.gz.
===========================================================================
=======================<phase: patch-depends  >============================
===========================================================================
=======================<phase: patch          >============================
===>  Patching for hdf5-1.6.9_2
===>  Applying FreeBSD patches for hdf5-1.6.9_2
===========================================================================
=======================<phase: build-depends  >============================
===>   hdf5-1.6.9_2 depends on package: libtool>=2.4 - not found
===>    Verifying install for libtool>=2.4 in /usr/ports/devel/libtool
===>   Installing existing package /packages/All/libtool-2.4.2_1.txz
Installing libtool-2.4.2_1... done
===>   Returning to build of hdf5-1.6.9_2
===========================================================================
=======================<phase: lib-depends    >============================
===========================================================================
=======================<phase: configure      >============================
===>  Configuring for hdf5-1.6.9_2
===>   FreeBSD 10 autotools fix applied to 
/wrkdirs/usr/ports/science/hdf5/work/hdf5-1.6.9/fortran/aclocal.m4
===>   FreeBSD 10 autotools fix applied to 
/wrkdirs/usr/ports/science/hdf5/work/hdf5-1.6.9/fortran/configure
===>   FreeBSD 10 autotools fix applied to 
/wrkdirs/usr/ports/science/hdf5/work/hdf5-1.6.9/c++/aclocal.m4
===>   FreeBSD 10 autotools fix applied to 
/wrkdirs/usr/ports/science/hdf5/work/hdf5-1.6.9/c++/configure
===>   FreeBSD 10 autotools fix applied to 
/wrkdirs/usr/ports/science/hdf5/work/hdf5-1.6.9/aclocal.m4
===>   FreeBSD 10 autotools fix applied to 
/wrkdirs/usr/ports/science/hdf5/work/hdf5-1.6.9/configure
configure: loading site script /usr/ports/Templates/config.site
checking build system type... i386-portbld-freebsd10.0
checking host system type... i386-portbld-freebsd10.0
checking shell variables initial values... done
checking if basename works... yes
checking if xargs works... yes
checking for cached host... none
checking for config i386-portbld-freebsd10.0... no
checking for config i386-portbld-freebsd... no
checking for config portbld-freebsd10.0... no
checking for config portbld-freebsd... no
checking for config i386-freebsd10.0... no
checking for config i386-freebsd... no
checking for config i386-portbld... no
checking for config freebsd10.0... no
checking for config freebsd... found
checking for config ./config/site-specific/host-head-i386-default-job-03... no
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 if fortran interface enabled... no
checking if c++ interface enabled... yes
checking if should build only statically linked executables... no
checking for perl... no
checking for ar... ar
checking whether make sets $(MAKE)... yes
checking for a BSD-compatible install... /usr/bin/install -c -o root -g wheel
checking for ld used by GCC... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking for /usr/bin/ld option to reload object files... -r
checking for BSD-compatible nm... /usr/bin/nm -B
checking whether ln -s works... yes
checking how to recognise dependant libraries... pass_all
checking command to parse /usr/bin/nm -B output... Segmentation fault
ok
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 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 for ranlib... ranlib
checking for strip... strip
checking for objdir... .libs
checking for cc option to produce PIC... -fPIC
checking if cc PIC flag -fPIC 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.lo... yes
checking if cc supports -fno-rtti -fno-exceptions... yes
checking whether the linker (/usr/bin/ld) supports shared libraries... yes
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
checking dynamic linker characteristics... freebsd10.0 ld.so
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... yes
<snip>
config.status: creating src/libhdf5.settings
config.status: creating config/depend1
config.status: creating config/depend2
config.status: creating config/depend3
config.status: creating config/depend4
config.status: creating config/dependN
config.status: creating config/commence
config.status: creating config/conclude
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating test/Makefile
config.status: creating perform/Makefile
config.status: creating tools/Makefile
config.status: creating tools/h5dump/Makefile
config.status: creating tools/h5dump/testh5dump.sh
config.status: creating tools/h5ls/testh5ls.sh
config.status: creating tools/h5import/Makefile
config.status: creating tools/h5diff/Makefile
config.status: creating tools/h5jam/Makefile
config.status: creating tools/h5jam/testh5jam.sh
config.status: creating tools/h5repack/Makefile
config.status: creating tools/h5repack/h5repack.sh
config.status: creating tools/h5ls/Makefile
config.status: creating tools/lib/Makefile
config.status: creating tools/misc/Makefile
config.status: creating tools/misc/h5cc
config.status: creating examples/Makefile
config.status: creating examples/testh5cc.sh
config.status: creating doc/Makefile
config.status: creating doc/html/Makefile
config.status: creating doc/html/ed_libs/Makefile
config.status: creating doc/html/ed_styles/Makefile
config.status: creating doc/html/ADGuide/Makefile
config.status: creating doc/html/Graphics/Makefile
config.status: creating doc/html/Intro/Makefile
config.status: creating doc/html/PSandPDF/Makefile
config.status: creating doc/html/TechNotes/Makefile
config.status: creating doc/html/Tutor/Makefile
config.status: creating doc/html/Tutor/Graphics/Makefile
config.status: creating doc/html/Tutor/examples/Makefile
config.status: creating doc/html/cpplus/Makefile
config.status: creating doc/html/cpplus_RM/Makefile
config.status: creating doc/html/cpplus_RM/header_files/Makefile
config.status: creating doc/html/fortran/Makefile
config.status: creating hl/Makefile
config.status: creating hl/examples/Makefile
config.status: creating hl/src/Makefile
config.status: creating hl/test/Makefile
config.status: creating hl/tools/Makefile
config.status: creating hl/tools/gif2h5/Makefile
config.status: creating src/H5config.h
config.status: executing default-1 commands
creating src/H5pubconf.h

Configure Summary
Compiling Options:
               Compilation Mode:  Production
                     C Compiler:  cc
                         CFLAGS:   -O2 -pipe -fno-strict-aliasing 
                       CPPFLAGS:  -UH5_DEBUG_API -DNDEBUG -D_XOPEN_SOURCE=600 
                        LDFLAGS:   -pthread
                     Debug Mode:  None
               Shared Libraries:  Yes
               Static Libraries:  Yes
  Statically Linked Executables:  No
                        Tracing:  No
   Optimization Instrumentation:  Yes

Languages:
----------
                            C++:  Yes
                   C++ Compiler:  c++
                       CXXFLAGS:   -O2 -pipe -fno-strict-aliasing 

                        Fortran:  No

Features:
---------
                        dmalloc:  No
         Function Stack Tracing:  Disabled
                           GPFS:  No
      Strict File Format Checks:  Enabled
        HDF5 v1.4 Compatibility:  No
         I/O filters (external):  deflate
         I/O filters (internal):  shuffle,fletcher32
 Linux Large File Support (LFS):  Disabled
                            MPE:  No
                  Parallel HDF5:  No
                   Threadsafety:  Enabled
             High Level library:  Enabled
===========================================================================
=======================<phase: build          >============================
===>  Building for hdf5-1.6.9_2
+ cd src
+ /usr/bin/make lib
mkdir .libs
cc -O2 -pipe -fno-strict-aliasing -I. -I. -UH5_DEBUG_API -DNDEBUG 
-D_XOPEN_SOURCE=600 -c ./H5.c  -fPIC -DPIC -o .libs/H5.lo
In file included from ./H5.c:19:
In file included from ./H5private.h:29:
./H5public.h:184:5: error: "nothing appropriate for haddr_t"
#   error "nothing appropriate for haddr_t"
    ^
In file included from ./H5.c:19:
./H5private.h:339:5: error: "nothing appropriate for int16_t"
#   error "nothing appropriate for int16_t"
    ^
./H5private.h:352:5: error: "nothing appropriate for uint16_t"
#   error "nothing appropriate for uint16_t"
    ^
./H5private.h:369:5: error: "nothing appropriate for int32_t"
#   error "nothing appropriate for int32_t"
    ^
./H5private.h:386:5: error: "nothing appropriate for uint32_t"
#   error "nothing appropriate for uint32_t"
    ^
./H5private.h:403:5: error: "nothing appropriate for int64_t"
#   error "nothing appropriate for int64_t"
    ^
./H5private.h:420:5: error: "nothing appropriate for uint64_t"
#   error "nothing appropriate for uint64_t"
    ^
./H5private.h:597:23: error: unknown type name 'FILE'
H5_DLL int HDfprintf (FILE *stream, const char *fmt, ...);
                      ^
./H5private.h:636:9: error: unknown type name 'off_t'
typedef off_t                   h5_stat_size_t;
        ^
./H5private.h:826:8: error: unknown type name 'int64_t'
H5_DLL int64_t HDstrtoll (const char *s, const char **rest, int base);
       ^
./H5private.h:904:65: error: unknown type name 'va_list'; did you mean 
'__va_list'?
H5_DLL int HDvsnprintf(char *buf, size_t size, const char *fmt, va_list ap);
                                                                ^~~~~~~
                                                                __va_list
./H5private.h:867:53: note: expanded from macro 'HDvsnprintf'
#   define HDvsnprintf(S,N,FMT,A) vsnprintf(S,N,FMT,A)
                                                    ^
/usr/include/x86/_types.h:154:27: note: '__va_list' declared here
typedef __builtin_va_list       __va_list;      /* internally known to gcc */
                                ^
In file included from ./H5.c:19:
./H5private.h:940:5: error: unknown type name 'FILE'
    FILE                *trace;         /*API trace output stream       */
    ^
./H5private.h:945:2: error: unknown type name 'FILE'
        FILE            *stream;        /*output stream or NULL         */
        ^
In file included from ./H5.c:20:
In file included from ./H5Bprivate.h:36:
In file included from ./H5ACprivate.h:39:
In file included from ./H5Fprivate.h:24:
./H5Fpublic.h:119:8: error: unknown type name 'hssize_t'; did you mean 
'ssize_t'?
H5_DLL hssize_t H5Fget_freespace(hid_t file_id);
       ^~~~~~~~
       ssize_t
./H5public.h:114:13: note: 'ssize_t' declared here
typedef int ssize_t;
            ^
In file included from ./H5.c:20:
In file included from ./H5Bprivate.h:36:
In file included from ./H5ACprivate.h:39:
In file included from ./H5Fprivate.h:24:
./H5Fpublic.h:120:46: error: unknown type name 'hsize_t'
H5_DLL herr_t H5Fget_filesize(hid_t file_id, hsize_t *size);
                                             ^
In file included from ./H5.c:20:
In file included from ./H5Bprivate.h:36:
In file included from ./H5ACprivate.h:39:
In file included from ./H5Fprivate.h:27:
./H5FDpublic.h:138:5: error: unknown type name 'haddr_t'
    haddr_t maxaddr;
    ^
./H5FDpublic.h:140:5: error: type name requires a specifier or qualifier
    hsize_t (*sb_size)(H5FD_t *file);
    ^
./H5FDpublic.h:140:15: warning: type specifier missing, defaults to 'int' 
[-Wimplicit-int]
    hsize_t (*sb_size)(H5FD_t *file);
             ~^
./H5FDpublic.h:140:13: error: function cannot return function type 'int (H5FD_t 
*)'
    hsize_t (*sb_size)(H5FD_t *file);
            ^
./H5FDpublic.h:152:21: error: unknown type name 'haddr_t'
                    haddr_t maxaddr);
                    ^
fatal error: too many errors emitted, stopping now [-ferror-limit=]
1 warning and 20 errors generated.
*** Error code 1

Stop.
make[2]: stopped in /wrkdirs/usr/ports/science/hdf5/work/hdf5-1.6.9/src
+ exit 1
*** Error code 1

Stop.
make[1]: stopped in /wrkdirs/usr/ports/science/hdf5/work/hdf5-1.6.9
*** Error code 1

Stop.
make: stopped in /usr/ports/science/hdf5
===>  Cleaning for hdf5-1.6.9_2
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