[MINC-users] Minc-2 installation problems
Simon Fristed Eskildsen
se at hst.aau.dk
Sun Apr 5 07:27:16 EDT 2009
Hi Mohamed,
Try using double quotation marks instead of single:
./configure --disable-shared --prefix=/usr/local --with-build-path=/usr/local CFLAGS="${CFLAGS} -fpic" CPPFLAGS="${CPPFLAGS} -fpic" CXXFLAGS="${CXXFLAGS} -fpic"
As far as I remember bash does not expand into single quatation marks. If it does not help, try exporting the flags before configuring:
export CFLAGS="${CFLAGS} -fpic"
export CPPFLAGS="${CPPFLAGS} -fpic"
export CXXFLAGS="${CXXFLAGS} -fpic"
./configure --disable-shared --prefix=/usr/local --with-build-path=/usr/local
Simon
----- "mohamed Ali Bahri" <m.bahri at ulg.ac.be> wrote:
> Hi Claude,
>
> I tried with your command line and it gave me the following error:
>
> -----------------------------------------------------------------------------------------------------------
> [root at localhost hdf5-1.6.6]# ./configure --disable-shared
> --prefix=/usr/local --with-build-path=/usr/local CFLAGS='${CFLAGS}
> -fpic' CPPFLAGS='${CPPFLAGS} -fpic' CXXFLAGS='${CXXFLAGS} -fpic'
> checking build system type... x86_64-unknown-linux-gnu
> checking host system type... x86_64-unknown-linux-gnu
> checking shell variables initial values... done
> checking if basename works... yes
> checking if xargs works... yes
> checking for cached host... none
> checking for sizeof hsize_t and hssize_t... large
> checking for config x86_64-unknown-linux-gnu... no
> checking for config x86_64-unknown-linux-gnu... no
> checking for config unknown-linux-gnu... no
> checking for config unknown-linux-gnu... no
> checking for config x86_64-linux-gnu... no
> checking for config x86_64-linux-gnu... no
> checking for config x86_64-unknown... no
> checking for config linux-gnu... found
> compiler 'gcc' is GNU gcc-4.3.0
> checking for config
> ./config/site-specific/host-localhost.localdomain... no
> checking for config ./config/site-specific/host-localdomain... no
> checking for gcc... gcc
> checking for C compiler default output file name...
> configure: error: C compiler cannot create executables
> See `config.log' for more details.
> ------------------------------------------------------------------------------------------------------
> As compiler I use gcc 4.3 (gcc (GCC) 4.3.0 20080428 (Red Hat
> 4.3.0-8).
> I also attached the config.log if this could give information about my
>
> problem.
>
> Thank you very much for your help
>
> Best regards
> Mohamed
>
>
>
>
>
> Claude LEPAGE a écrit :
> > Hi,
> >
> >
> >> Thank you for your answer. I tried to use HDF5-1.6.6 instead of
> >> hdf5-1.8.2 but now I have errors with HDF5.
> >> I use the following command lines:
> >>
> >> 1) FC=/usr/bin/gfortran ./configure --prefix=/usr/local/
> >> --with-zlib=/usr/local/ --enable-fortran --enable-cxx
> >> 2) make
> >>
> >
> > Here is how I compile HDF5-1.6.6 in 64 bits Linux:
> >
> > ./configure --disable-shared --prefix=/usr/local
> --with-build-path=/usr/local CFLAGS='${CFLAGS} -fpic'
> CPPFLAGS='${CPPFLAGS} -fpic' CXXFLAGS='${CXXFLAGS} -fpic'
> > make
> > make install
> >
> > --disable-shared is optional
> > no need to fuss about fortran (not needed by minc2)
> >
> > By the way, which compiler are you using? It looks like your C++
> > compiler does not like the code. Strange...
> >
> > gcc --version
> >
> > minc2 may compile with gcc 4.2+, but not all MNI tools do (yet).
> >
> > Claude
> >
> >
> >
> >> ===============================================
> >>
> >> g++ -O2 -I. -I../../src -I../../src -D_BSD_SOURCE -D_POSIX_SOURCE
> >> -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE
> >> -I/usr/local//include -c H5PropList.cpp -fPIC -DPIC -o
> .libs/H5PropList.lo
> >> H5PropList.cpp: In member function 'std::string
> >> H5::PropList::getClassName() const':
> >> H5PropList.cpp:428: error: 'free' was not declared in this scope
> >> make[3]: *** [H5PropList.lo] Erreur 1
> >> make[3]: quittant le répertoire « /usr/local/hdf5-1.6.6/c++/src »
> >> make[2]: *** [lib] Erreur 1
> >> make[2]: quittant le répertoire « /usr/local/hdf5-1.6.6/c++ »
> >> make[1]: *** [lib] Erreur 1
> >> make[1]: quittant le répertoire « /usr/local/hdf5-1.6.6 »
> >> make: *** [all] Erreur 2
> >> =======================================================
> >>
> >> Thanks a lot,
> >> Mohamed
> >>
> >> Claude LEPAGE a écrit :
> >>
> >>> Hi,
> >>>
> >>>
> >>>
> >>>> I have a problem with minc-2.0.17 installation (make command
> fails). Any
> >>>> one have an idea how I can solve that?
> >>>> I use linux (Fedora 9, 64-bit).
> >>>>
> >>>> libtool: compile: gcc -DHAVE_CONFIG_H -I. -I./libsrc
> >>>> -I./volume_io/Include -I./volume_io/Include -I./progs/Proglib
> >>>> -I./conversion/Acr_nema -I./libsrc2 -g -O2 -MT
> libsrc/hdf_convenience.lo
> >>>> -MD -MP -MF libsrc/.deps/hdf_convenience.Tpo -c
> libsrc/hdf_convenience.c
> >>>> -o libsrc/hdf_convenience.o
> >>>> libsrc/hdf_convenience.c: In function ‘hdf_id_add’:
> >>>> libsrc/hdf_convenience.c:83: erreur: too few arguments to
> function
> >>>> ‘H5Gopen2’
> >>>> libsrc/hdf_convenience.c: In function ‘hdf_var_add’:
> >>>> libsrc/hdf_convenience.c:185: erreur: too few arguments to
> function
> >>>>
> >>>>
> >>> I haven't seen this problem, but here is an idea.
> >>>
> >>> Which version of HDF5 have you installed? minc2 has been tested
> >>> with HDF5 up to 5-1.6.7. If you are using 5-1.8.X, I would
> suggest
> >>> to try 5-1.6.6 (what I am currently using) or 5-1.6.7. If I
> recall,
> >>> 5-1.8.X is not 100% compatible with previous versions.
> >>>
> >>> The problem may be different too, but making sure you are using
> >>> a compatible version of HDF5 is the first step.
> >>>
> >>> Yours,
> >>>
> >>> Claude
> >>>
> >>>
> >>>
> ------------------------------------------------------------------------
> >>>
> >>> _______________________________________________
> >>> MINC-users at bic.mni.mcgill.ca
> >>> http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> >>>
> >>>
> >> _______________________________________________
> >> MINC-users at bic.mni.mcgill.ca
> >> http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> >>
> >>
> >>
> ------------------------------------------------------------------------
> >>
> >> _______________________________________________
> >> MINC-users at bic.mni.mcgill.ca
> >> http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> >>
>
>
> This file contains any messages produced by compilers while
> running configure, to aid debugging if configure makes a mistake.
>
> It was created by HDF5 configure 1.6.6, which was
> generated by GNU Autoconf 2.61. Invocation command line was
>
> $ ./configure --disable-shared --prefix=/usr/local
> --with-build-path=/usr/local CFLAGS=${CFLAGS} -fpic
> CPPFLAGS=${CPPFLAGS} -fpic CXXFLAGS=${CXXFLAGS} -fpic
>
> ## --------- ##
> ## Platform. ##
> ## --------- ##
>
> hostname = localhost.localdomain
> uname -m = x86_64
> uname -r = 2.6.27.21-78.2.41.fc9.x86_64
> uname -s = Linux
> uname -v = #1 SMP Mon Mar 23 23:22:15 EDT 2009
>
> /usr/bin/uname -p = unknown
> /bin/uname -X = unknown
>
> /bin/arch = x86_64
> /usr/bin/arch -k = unknown
> /usr/convex/getsysinfo = unknown
> /usr/bin/hostinfo = unknown
> /bin/machine = unknown
> /usr/bin/oslevel = unknown
> /bin/universe = unknown
>
> PATH: /usr/kerberos/sbin
> PATH: /usr/
> PATH: /home/Mohamed/Bureau/Sources_Codes/camino/bin
> PATH: /usr/java/latest/bin
> PATH: /usr/
> PATH: /home/Mohamed/Bureau/Sources_Codes/camino/bin
> PATH: /usr/java/latest/bin
> PATH: /usr/lib64/qt-3.3/bin
> PATH: /usr/kerberos/bin
> PATH: /usr/lib64/ccache
> PATH: /usr/local/bin
> PATH: /usr/bin
> PATH: /bin
> PATH: /home/Mohamed/Bureau/Sources_Codes/bin_lnx
> PATH: /home/Mohamed/Bureau/Sources_Codes/bin
> PATH: /home/Mohamed/Bureau/Sources_Codes/pvelab-20080317/Canterbury
> PATH: /usr/local/caret/bin
> PATH: /usr/local/bin
> PATH: /home/Mohamed/bin
> PATH: /home/Mohamed/Bureau/Sources_Codes/bin_lnx
> PATH: /home/Mohamed/Bureau/Sources_Codes/bin
> PATH: /home/Mohamed/Bureau/Sources_Codes/pvelab-20081112/Canterbury
> PATH: /usr/local/caret/bin
>
>
> ## ----------- ##
> ## Core tests. ##
> ## ----------- ##
>
> configure:2034: checking build system type
> configure:2052: result: x86_64-unknown-linux-gnu
> configure:2074: checking host system type
> configure:2089: result: x86_64-unknown-linux-gnu
> configure:2119: checking shell variables initial values
> BASH=/bin/sh
> BASH_ARGC=([0]="6")
> BASH_ARGV=([0]="CXXFLAGS=\${CXXFLAGS} -fpic"
> [1]="CPPFLAGS=\${CPPFLAGS} -fpic" [2]="CFLAGS=\${CFLAGS} -fpic"
> [3]="--with-build-path=/usr/local" [4]="--prefix=/usr/local"
> [5]="--disable-shared")
> BASH_LINENO=([0]="0")
> BASH_SOURCE=([0]="./configure")
> BASH_VERSINFO=([0]="3" [1]="2" [2]="33" [3]="1" [4]="release"
> [5]="x86_64-redhat-linux-gnu")
> BASH_VERSION='3.2.33(1)-release'
> CCACHE_DIR=/var/cache/ccache
> CCACHE_UMASK=002
> CFLAGS='${CFLAGS} -fpic'
> COLORTERM=gnome-terminal
> CPPFLAGS='${CPPFLAGS} -fpic'
> CVS_RSH=ssh
> CXXFLAGS='${CXXFLAGS} -fpic'
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> GROUPS=()
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> IFS='
> '
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> LANGUAGE=C
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> LC_PAPER=C
> LC_TELEPHONE=C
> LC_TIME=C
> LESSOPEN='|/usr/bin/lesspipe.sh %s'
> LIBOBJS=
> LINENO=2119
> LOGNAME=Mohamed
> LS_COLORS='no=00:fi=00:di=00;34:ln=00;36:pi=40;33:so=00;35:do=00;35:bd=40;33;01:cd=40;33;01:or=40;31;01:mi=01;05;37;41:su=37;41:sg=30;43:tw=30;42:ow=34;42:st=37;44:ex=00;32:*.cmd=00;32:*.exe=00;32:*.com=00;32:*.btm=00;32:*.bat=00;32:*.sh=00;32:*.csh=00;32:*.tar=00;31:*.tgz=00;31:*.svgz=00;31:*.arj=00;31:*.taz=00;31:*.lzh=00;31:*.lzma=00;31:*.zip=00;31:*.z=00;31:*.Z=00;31:*.dz=00;31:*.gz=00;31:*.bz2=00;31:*.tbz2=00;31:*.bz=00;31:*.tz=00;31:*.deb=00;31:*.rpm=00;31:*.jar=00;31:*.rar=00;31:*.ace=00;31:*.zoo=00;31:*.cpio=00;31:*.7z=00;31:*.rz=00;31:*.jpg=00;35:*.jpeg=00;35:*.gif=00;35:*.bmp=00;35:*.pbm=00;35:*.pgm=00;35:*.ppm=00;35:*.tga=00;35:*.xbm=00;35:*.xpm=00;35:*.tif=00;35:*.tiff=00;35:*.png=00;35:*.mng=00;35:*.pcx=00;35:*.mov=00;35:*.mpg=00;35:*.mpeg=00;35:*.m2v=00;35:*.mkv=00;35:*.ogm=00;35:*.mp4=00;35:*.m4v=00;35:*.mp4v=00;35:*.vob=00;35:*.qt=00;35:*.nuv=00;35:*.wmv=00;35:*.asf=00;35:*.rm=00;35:*.rmvb=00;35:*.flc=00;35:*.avi=00;35:*.fli=00;35:*.gl=00;35:*.dl=00;35:*.xcf=00;35:*.xwd=00;35:*.yuv=00;35:*.svg=00;35:*.aac=00;36:*.au=00;36:*.flac=00;36:*.mid=00;36:*.midi=00;36:*.mka=00;36:*.mp3=00;36:*.mpc=00;36:*.ogg=00;36:*.ra=00;36:*.wav=00;36:'
> MACHTYPE=x86_64-redhat-linux-gnu
> MAKEFLAGS=
> MANPATH=/home/Mohamed/Bureau/Sources_Codes/camino/man:/home/Mohamed/Bureau/Sources_Codes/camino/man:
> MFLAGS=
> OPTERR=1
> OPTIND=1
> OSTYPE=linux-gnu
> PACKAGE_BUGREPORT=help at hdfgroup.org
> PACKAGE_NAME=HDF5
> PACKAGE_STRING='HDF5 1.6.6'
> PACKAGE_TARNAME=hdf5
> PACKAGE_VERSION=1.6.6
> PATH=/usr/kerberos/sbin:/usr/:/home/Mohamed/Bureau/Sources_Codes/camino/bin:/usr/java/latest/bin:/usr/:/home/Mohamed/Bureau/Sources_Codes/camino/bin:/usr/java/latest/bin:/usr/lib64/qt-3.3/bin:/usr/kerberos/bin:/usr/lib64/ccache:/usr/local/bin:/usr/bin:/bin:/home/Mohamed/Bureau/Sources_Codes/bin_lnx:/home/Mohamed/Bureau/Sources_Codes/bin:/home/Mohamed/Bureau/Sources_Codes/pvelab-20080317/Canterbury:/usr/local/caret/bin:/usr/local/bin:/home/Mohamed/bin:/home/Mohamed/Bureau/Sources_Codes/bin_lnx:/home/Mohamed/Bureau/Sources_Codes/bin:/home/Mohamed/Bureau/Sources_Codes/pvelab-20081112/Canterbury:/usr/local/caret/bin
> PATH_SEPARATOR=:
> PIPESTATUS=([0]="0")
> POSIXLY_CORRECT=y
> PPID=18841
> PS1='$ '
> PS2='> '
> PS4='+ '
> PWD=/usr/local/hdf5-1.6.6
> QTDIR=/usr/lib64/qt-3.3
> QTINC=/usr/lib64/qt-3.3/include
> QTLIB=/usr/lib64/qt-3.3/lib
> QT_PLUGIN_PATH=/home/Mohamed/.kde/lib64/kde4/plugins/:/usr/lib64/kde4/plugins/:/home/Mohamed/.kde/lib64/kde4/plugins/:/usr/lib64/kde4/plugins/:/root/.kde/lib64/kde4/plugins/:/usr/lib64/kde4/plugins/
> SDL_AUDIODRIVER=esd
> SESSION_MANAGER=local/unix:@/tmp/.ICE-unix/3102,unix/unix:/tmp/.ICE-unix/3102
> SHELL=/bin/sh
> SHELLOPTS=braceexpand:hashall:interactive-comments:posix
> SHLVL=5
> SSH_AGENT_PID=3004
> SSH_ASKPASS=/usr/libexec/openssh/gnome-ssh-askpass
> SSH_AUTH_SOCK=/tmp/ssh-HrNOIy2989/agent.2989
> TERM=xterm
> UID=0
> USER=Mohamed
> USERNAME=Mohamed
> WINDOWID=69352330
> XAUTHORITY=/root/.xauthKzN42J
> XCURSOR_THEME=default
> XDG_DATA_DIRS=/usr/share/kde-settings/kde-profile/default/share:/usr/local/share:/usr/share
> XDG_MENU_PREFIX=kde4-
> XDG_SESSION_COOKIE=3c9951686a5e8d532a63fd49483d59e3-1238857151.730932-316909989
> _='checking shell variables initial values... '
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> ac_arg='CPPFLAGS=${CPPFLAGS} -fpic'
> ac_aux_dir=bin
> ac_build_alias=x86_64-unknown-linux-gnu
> ac_cache_corrupted=false
> ac_clean_files=
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> '\''--prefix=/usr/local'\'' '\''--with-build-path=/usr/local'\''
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> '\''CXXFLAGS=${CXXFLAGS} -fpic'\'''
> ac_cpp='$CPP $CPPFLAGS'
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> ac_cv_env_CC_value=
> ac_cv_env_CFLAGS_set=set
> ac_cv_env_CFLAGS_value='${CFLAGS} -fpic'
> ac_cv_env_CPPFLAGS_set=set
> ac_cv_env_CPPFLAGS_value='${CPPFLAGS} -fpic'
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> ac_cv_host=x86_64-unknown-linux-gnu
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> ac_default_prefix=/usr/local/hdf5-1.6.6/hdf5
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> SRB
> TESTSRB
> PTHREAD
> DEBUG_PKG
> TRACE_API
> INSTRUMENT_LIBRARY
> CLEARFILEBUF
> MPE
> MPI_GET_SIZE
> FILTERS
> USE_FILTER_SHUFFLE
> USE_FILTER_FLETCHER32
> H5_VERSION
> CONFIG_DATE
> CONFIG_USER
> CONFIG_MODE
> BYTESEX
> STATIC_SHARED
> CC_VERSION
> ROOT
> DYNAMIC_DIRS
> HL
> SEARCH
> SETX
> LIBOBJS
> LTLIBOBJS'
> ac_tool_prefix=
> ac_unique_file=src/H5.c
> ac_val='${datarootdir}/man'
> ac_var=CPP
> as_basename=basename
> as_cr_LETTERS=ABCDEFGHIJKLMNOPQRSTUVWXYZ
> as_cr_Letters=abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ
> as_cr_alnum=abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ0123456789
> as_cr_digits=0123456789
> as_cr_letters=abcdefghijklmnopqrstuvwxyz
> as_dir=/usr/local/caret/bin
> as_dirname=dirname
> as_executable_p='test -x'
> as_expr=expr
> as_have_required=yes
> as_lineno_1=426
> as_lineno_2=427
> as_ln_s='ln -s'
> as_me=configure
> as_mkdir_p=:
> as_myself=./configure
> as_nl='
> '
> as_save_IFS='
> '
> as_test_x='test -x'
> as_tr_cpp='eval sed
> '\''y%*abcdefghijklmnopqrstuvwxyz%PABCDEFGHIJKLMNOPQRSTUVWXYZ%;s%[^_abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ0123456789]%_%g'\'''
> as_tr_sh='eval sed
> '\''y%*+%pp%;s%[^_abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ0123456789]%_%g'\'''
> as_unset=unset
> as_var=LC_TIME
> bindir='${exec_prefix}/bin'
> build=x86_64-unknown-linux-gnu
> build_cpu=x86_64
> build_os=linux-gnu
> build_vendor=unknown
> cache_file=/dev/null
> cmd='sed 50q "$0"'
> cross_compiling=no
> datadir='${datarootdir}'
> datarootdir='${prefix}/share'
> docdir='${datarootdir}/doc/${PACKAGE_TARNAME}'
> dvidir='${docdir}'
> echo=echo
> echo_test_string='#! /bin/sh
> # From configure.in Id: configure.in 14063 2007-08-09 20:51:55Z
> mcgreevy .
> # Guess values for system-dependent variables and create Makefiles.
> # Generated by GNU Autoconf 2.61 for HDF5 1.6.6.
> #
> # Report bugs to <help at hdfgroup.org>.
> #
> # Copyright (C) 1992, 1993, 1994, 1995, 1996, 1998, 1999, 2000, 2001,
> # 2002, 2003, 2004, 2005, 2006 Free Software Foundation, Inc.
> # This configure script is free software; the Free Software
> Foundation
> # gives unlimited permission to copy, distribute and modify it.
> ## --------------------- ##
> ## M4sh Initialization. ##
> ## --------------------- ##
>
> # Be more Bourne compatible
> DUALCASE=1; export DUALCASE # for MKS sh
> if test -n "${ZSH_VERSION+set}" && (emulate sh) >/dev/null 2>&1; then
> emulate sh
> NULLCMD=:
> # Zsh 3.x and 4.x performs word splitting on ${1+"$@"}, which
> # is contrary to our usage. Disable this feature.
> alias -g '\''${1+"$@"}'\''='\''"$@"'\''
> setopt NO_GLOB_SUBST
> else
> case `(set -o) 2>/dev/null` in
> *posix*) set -o posix ;;
> esac
>
> fi
>
>
>
>
> # PATH needs CR
> # Avoid depending upon Character Ranges.
> as_cr_letters='\''abcdefghijklmnopqrstuvwxyz'\''
> as_cr_LETTERS='\''ABCDEFGHIJKLMNOPQRSTUVWXYZ'\''
> as_cr_Letters=$as_cr_letters$as_cr_LETTERS
> as_cr_digits='\''0123456789'\''
> as_cr_alnum=$as_cr_Letters$as_cr_digits
>
> # The user is always right.
> if test "${PATH_SEPARATOR+set}" != set; then
> echo "#! /bin/sh" >conf$$.sh
> echo "exit 0" >>conf$$.sh
> chmod +x conf$$.sh
> if (PATH="/nonexistent;."; conf$$.sh) >/dev/null 2>&1; then
> PATH_SEPARATOR='\'';'\''
> else'
> echo_testing_string='#! /bin/sh
> # From configure.in Id: configure.in 14063 2007-08-09 20:51:55Z
> mcgreevy .
> # Guess values for system-dependent variables and create Makefiles.
> # Generated by GNU Autoconf 2.61 for HDF5 1.6.6.
> #
> # Report bugs to <help at hdfgroup.org>.
> #
> # Copyright (C) 1992, 1993, 1994, 1995, 1996, 1998, 1999, 2000, 2001,
> # 2002, 2003, 2004, 2005, 2006 Free Software Foundation, Inc.
> # This configure script is free software; the Free Software
> Foundation
> # gives unlimited permission to copy, distribute and modify it.
> ## --------------------- ##
> ## M4sh Initialization. ##
> ## --------------------- ##
>
> # Be more Bourne compatible
> DUALCASE=1; export DUALCASE # for MKS sh
> if test -n "${ZSH_VERSION+set}" && (emulate sh) >/dev/null 2>&1; then
> emulate sh
> NULLCMD=:
> # Zsh 3.x and 4.x performs word splitting on ${1+"$@"}, which
> # is contrary to our usage. Disable this feature.
> alias -g '\''${1+"$@"}'\''='\''"$@"'\''
> setopt NO_GLOB_SUBST
> else
> case `(set -o) 2>/dev/null` in
> *posix*) set -o posix ;;
> esac
>
> fi
>
>
>
>
> # PATH needs CR
> # Avoid depending upon Character Ranges.
> as_cr_letters='\''abcdefghijklmnopqrstuvwxyz'\''
> as_cr_LETTERS='\''ABCDEFGHIJKLMNOPQRSTUVWXYZ'\''
> as_cr_Letters=$as_cr_letters$as_cr_LETTERS
> as_cr_digits='\''0123456789'\''
> as_cr_alnum=$as_cr_Letters$as_cr_digits
>
> # The user is always right.
> if test "${PATH_SEPARATOR+set}" != set; then
> echo "#! /bin/sh" >conf$$.sh
> echo "exit 0" >>conf$$.sh
> chmod +x conf$$.sh
> if (PATH="/nonexistent;."; conf$$.sh) >/dev/null 2>&1; then
> PATH_SEPARATOR='\'';'\''
> else'
> enable_shared=no
> exec_prefix=NONE
> host=x86_64-unknown-linux-gnu
> host_cpu=x86_64
> host_os=linux-gnu
> host_vendor=unknown
> htmldir='${docdir}'
> includedir='${prefix}/include'
> infodir='${datarootdir}/info'
> libdir='${exec_prefix}/lib'
> libexecdir='${exec_prefix}/libexec'
> localedir='${datarootdir}/locale'
> localstatedir='${prefix}/var'
> mandir='${datarootdir}/man'
> no_create=
> no_recursion=
> oldincludedir=/usr/include
> pdfdir='${docdir}'
> prefix=/usr/local
> program_prefix=NONE
> program_suffix=NONE
> program_transform_name=s,x,x,
> psdir='${docdir}'
> sbindir='${exec_prefix}/sbin'
> sharedstatedir='${prefix}/com'
> silent=
> site=
> srcdir=.
> subdirs=
> sysconfdir='${prefix}/etc'
> target=
> verbose=
> with_build_path=/usr/local
> x_includes=NONE
> x_libraries=NONE
> configure:2122: result: done
> configure:2127: checking if basename works
> configure:2135: result: yes
> configure:2139: checking if xargs works
> configure:2147: result: yes
> configure:2151: checking for cached host
> configure:2158: result: none
> configure:2200: checking for sizeof hsize_t and hssize_t
> configure:2203: result: large
> configure:2224: checking for config x86_64-unknown-linux-gnu
> configure:2232: result: no
> configure:2224: checking for config x86_64-unknown-linux-gnu
> configure:2232: result: no
> configure:2224: checking for config unknown-linux-gnu
> configure:2232: result: no
> configure:2224: checking for config unknown-linux-gnu
> configure:2232: result: no
> configure:2224: checking for config x86_64-linux-gnu
> configure:2232: result: no
> configure:2224: checking for config x86_64-linux-gnu
> configure:2232: result: no
> configure:2224: checking for config x86_64-unknown
> configure:2232: result: no
> configure:2224: checking for config linux-gnu
> configure:2228: result: found
> configure:2243: checking for config
> ./config/site-specific/host-localhost.localdomain
> configure:2251: result: no
> configure:2243: checking for config
> ./config/site-specific/host-localdomain
> configure:2251: result: no
> configure:2306: checking for gcc
> configure:2333: result: gcc
> configure:2571: checking for C compiler version
> configure:2578: gcc --version >&5
> gcc (GCC) 4.3.0 20080428 (Red Hat 4.3.0-8)
> Copyright (C) 2008 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.
>
> configure:2581: $? = 0
> configure:2588: gcc -v >&5
> Using built-in specs.
> Target: x86_64-redhat-linux
> Configured with: ../configure --prefix=/usr --mandir=/usr/share/man
> --infodir=/usr/share/info
> --with-bugurl=http://bugzilla.redhat.com/bugzilla --enable-bootstrap
> --enable-shared --enable-threads=posix --enable-checking=release
> --with-system-zlib --enable-__cxa_atexit
> --disable-libunwind-exceptions
> --enable-languages=c,c++,objc,obj-c++,java,fortran,ada
> --enable-java-awt=gtk --disable-dssi --enable-plugin
> --with-java-home=/usr/lib/jvm/java-1.5.0-gcj-1.5.0.0/jre
> --enable-libgcj-multifile --enable-java-maintainer-mode
> --with-ecj-jar=/usr/share/java/eclipse-ecj.jar
> --disable-libjava-multilib --with-cpu=generic
> --build=x86_64-redhat-linux
> Thread model: posix
> gcc version 4.3.0 20080428 (Red Hat 4.3.0-8) (GCC)
> configure:2591: $? = 0
> configure:2598: gcc -V >&5
> gcc: '-V' option must have argument
> configure:2601: $? = 1
> configure:2624: checking for C compiler default output file name
> configure:2651: gcc ${CFLAGS} -fpic -ansi ${CPPFLAGS} -fpic
> conftest.c >&5
> gcc: ${CFLAGS}: No such file or directory
> gcc: ${CPPFLAGS}: No such file or directory
> configure:2654: $? = 1
> configure:2692: result:
> configure: failed program was:
> | /* confdefs.h. */
> | #define PACKAGE_NAME "HDF5"
> | #define PACKAGE_TARNAME "hdf5"
> | #define PACKAGE_VERSION "1.6.6"
> | #define PACKAGE_STRING "HDF5 1.6.6"
> | #define PACKAGE_BUGREPORT "help at hdfgroup.org"
> | #define HAVE_LARGE_HSIZET 1
> | /* end confdefs.h. */
> |
> | int
> | main ()
> | {
> |
> | ;
> | return 0;
> | }
> configure:2699: error: C compiler cannot create executables
> See `config.log' for more details.
>
> ## ---------------- ##
> ## Cache variables. ##
> ## ---------------- ##
>
> ac_cv_build=x86_64-unknown-linux-gnu
> ac_cv_env_CC_set=
> ac_cv_env_CC_value=
> ac_cv_env_CFLAGS_set=set
> ac_cv_env_CFLAGS_value='${CFLAGS} -fpic'
> ac_cv_env_CPPFLAGS_set=set
> ac_cv_env_CPPFLAGS_value='${CPPFLAGS} -fpic'
> ac_cv_env_CPP_set=
> ac_cv_env_CPP_value=
> ac_cv_env_LDFLAGS_set=
> ac_cv_env_LDFLAGS_value=
> ac_cv_env_LIBS_set=
> ac_cv_env_LIBS_value=
> ac_cv_env_build_alias_set=
> ac_cv_env_build_alias_value=
> ac_cv_env_host_alias_set=
> ac_cv_env_host_alias_value=
> ac_cv_env_target_alias_set=
> ac_cv_env_target_alias_value=
> ac_cv_host=x86_64-unknown-linux-gnu
> ac_cv_prog_ac_ct_CC=gcc
> hdf5_cv_host=x86_64-unknown-linux-gnu
>
> ## ----------------- ##
> ## Output variables. ##
> ## ----------------- ##
>
> AR=''
> BUILD_PARALLEL_CONDITIONAL_FALSE=''
> BUILD_PARALLEL_CONDITIONAL_TRUE=''
> BYTESEX=''
> CC='gcc'
> CC_VERSION=''
> CFLAGS='${CFLAGS} -fpic -ansi'
> CLEARFILEBUF=''
> CONFIG_DATE=''
> CONFIG_MODE=''
> CONFIG_USER=''
> CPP=''
> CPPFLAGS='${CPPFLAGS} -fpic'
> DEBUG_PKG=''
> DEFAULT_LIBS=''
> DEFS=''
> DYNAMIC_DIRS=''
> ECHO='echo'
> ECHO_C=''
> ECHO_N='-n'
> ECHO_T=''
> EGREP=''
> EXEEXT=''
> FILTERS=''
> GASS=''
> GREP=''
> H5_CFLAGS=''
> H5_CPPFLAGS=''
> H5_VERSION=''
> HL=''
> HSIZET='large'
> INSTALL_DATA=''
> INSTALL_PROGRAM=''
> INSTALL_SCRIPT=''
> INSTRUMENT_LIBRARY=''
> LDFLAGS=''
> LIBOBJS=''
> LIBS=''
> LIBTOOL=''
> LN_S=''
> LTLIBOBJS=''
> LT_STATIC_EXEC=''
> MPE=''
> MPI_GET_SIZE=''
> OBJEXT=''
> PACKAGE_BUGREPORT='help at hdfgroup.org'
> PACKAGE_NAME='HDF5'
> PACKAGE_STRING='HDF5 1.6.6'
> PACKAGE_TARNAME='hdf5'
> PACKAGE_VERSION='1.6.6'
> PARALLEL=''
> PATH_SEPARATOR=':'
> PERL=''
> PTHREAD=''
> RANLIB=''
> ROOT=''
> RUNPARALLEL=''
> RUNSERIAL=''
> SEARCH=''
> SETX=''
> SET_MAKE=''
> SHELL='/bin/sh'
> SRB=''
> SSL=''
> STATIC_SHARED=''
> STRIP=''
> TESTGASS=''
> TESTPARALLEL=''
> TESTSRB=''
> TRACE_API=''
> USE_FILTER_DEFLATE=''
> USE_FILTER_FLETCHER32=''
> USE_FILTER_SHUFFLE=''
> USE_FILTER_SZIP=''
> ac_ct_CC='gcc'
> bindir='${exec_prefix}/bin'
> build='x86_64-unknown-linux-gnu'
> build_alias=''
> build_cpu='x86_64'
> build_os='linux-gnu'
> build_vendor='unknown'
> config_dirs=''
> datadir='${datarootdir}'
> datarootdir='${prefix}/share'
> docdir='${datarootdir}/doc/${PACKAGE_TARNAME}'
> dvidir='${docdir}'
> exec_prefix='NONE'
> host='x86_64-unknown-linux-gnu'
> host_alias=''
> host_cpu='x86_64'
> host_os='linux-gnu'
> host_vendor='unknown'
> htmldir='${docdir}'
> includedir='${prefix}/include'
> infodir='${datarootdir}/info'
> libdir='${exec_prefix}/lib'
> libexecdir='${exec_prefix}/libexec'
> localedir='${datarootdir}/locale'
> localstatedir='${prefix}/var'
> mandir='${datarootdir}/man'
> oldincludedir='/usr/include'
> pdfdir='${docdir}'
> prefix='/usr/local'
> program_transform_name='s,x,x,'
> psdir='${docdir}'
> sbindir='${exec_prefix}/sbin'
> sharedstatedir='${prefix}/com'
> subdirs=''
> sysconfdir='${prefix}/etc'
> target_alias=''
>
> ## ------------------- ##
> ## File substitutions. ##
> ## ------------------- ##
>
> COMMENCE=''
> CONCLUDE=''
> DEPEND=''
>
> ## ----------- ##
> ## confdefs.h. ##
> ## ----------- ##
>
> #define PACKAGE_NAME "HDF5"
> #define PACKAGE_TARNAME "hdf5"
> #define PACKAGE_VERSION "1.6.6"
> #define PACKAGE_STRING "HDF5 1.6.6"
> #define PACKAGE_BUGREPORT "help at hdfgroup.org"
> #define HAVE_LARGE_HSIZET 1
>
> configure: exit 77
>
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users
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