[MINC-users] Minc-2 installation problems

[mohamed Ali Bahri]

Hi Simon,

Thank you very much for your suggestions, configure passes now without 
error but make check gave the following error:
Is it important that make check passes all tests?
Which version of netcdf should I install? and should I use the same 
options for configuration?

Thanks a lot,

make check errors
---------------------------------------------------------------------------------------------------------
Testing random sw long double -> float conversions                    
*FAILED*
HDF5-DIAG: Error detected in HDF5 library version: 1.6.6 thread 0.  Back 
trace follows.
  #000: H5T.c line 2435 in H5Tconvert(): unable to convert between src 
and dst data types
    major(13): Datatype interface
    minor(29): Unable to initialize object
  #001: H5T.c line 3984 in H5T_path_find(): no appropriate function for 
conversion path
    major(13): Datatype interface
    minor(29): Unable to initialize object
Testing random sw long double -> double conversions                   
*FAILED*
HDF5-DIAG: Error detected in HDF5 library version: 1.6.6 thread 0.  Back 
trace follows.
  #000: H5T.c line 2435 in H5Tconvert(): unable to convert between src 
and dst data types
    major(13): Datatype interface
    minor(29): Unable to initialize object
  #001: H5T.c line 3984 in H5T_path_find(): no appropriate function for 
conversion path
    major(13): Datatype interface
    minor(29): Unable to initialize object
***** 164 FAILURES! *****
1.55user 0.10system 0:01.66elapsed 99%CPU (0avgtext+0avgdata 0maxresident)k
0inputs+1088outputs (0major+20505minor)pagefaults 0swaps
make[2]: *** [_check-s] Erreur 1
make[2]: quittant le répertoire « /usr/local/hdf5-1.6.6/test »
make[1]: *** [check] Erreur 2
make[1]: quittant le répertoire « /usr/local/hdf5-1.6.6/test »
make: *** [check] Erreur 1
------------------------------------------------------------------------------------------------------------------

Mohamed


Simon Fristed Eskildsen a écrit :
> 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'
>> DBUS_SESSION_BUS_ADDRESS=unix:abstract=/tmp/dbus-qhDa2Oiw19,guid=4739190599a2a029607aa83c49d775c0
>> DEFAULT_LIBS=
>> DESKTOP_SESSION=kde
>> DESKTOP_STARTUP_ID=
>> DIRSTACK=()
>> DISPLAY=:0.0
>> DUALCASE=1
>> ECHO=echo
>> ECHO_C=
>> ECHO_N=-n
>> ECHO_T=
>> EUID=0
>> GDMSESSION=kde
>> GDM_LANG=fr_FR.UTF-8
>> GNOME_KEYRING_PID=2988
>> GNOME_KEYRING_SOCKET=/tmp/keyring-CdaPEr/socket
>> GPG_AGENT_INFO=/tmp/gpg-aiPs2p/S.gpg-agent:3059:1
>> GROUPS=()
>> GS_LIB=
>> GTK2_RC_FILES=/etc/gtk-2.0/gtkrc:/home/Mohamed/.gtkrc-2.0::/home/Mohamed/.kde/share/config/gtkrc-2.0
>> GTK_RC_FILES=/etc/gtk/gtkrc:/home/Mohamed/.gtkrc::/home/Mohamed/.kde/share/config/gtkrc
>> G_BROKEN_FILENAMES=1
>> HISTSIZE=1000
>> HOME=/root
>> HOSTNAME=localhost.localdomain
>> HOSTTYPE=x86_64
>> IFS=' 	
>> '
>> INPUTRC=/etc/inputrc
>> KDEDIRS=/usr
>> KDE_FULL_SESSION=true
>> KDE_IS_PRELINKED=1
>> KDE_MULTIHEAD=false
>> KDE_SESSION_UID=500
>> KDE_SESSION_VERSION=4
>> LANG=C
>> LANGUAGE=C
>> LC_ADDRESS=C
>> LC_ALL=C
>> LC_COLLATE=C
>> LC_CTYPE=C
>> LC_IDENTIFICATION=C
>> LC_MEASUREMENT=C
>> LC_MESSAGES=C
>> LC_MONETARY=C
>> LC_NAME=C
>> LC_NUMERIC=C
>> 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... '
>> ac_abs_confdir=/usr/local/hdf5-1.6.6
>> ac_arg='CPPFLAGS=${CPPFLAGS} -fpic'
>> ac_aux_dir=bin
>> ac_build_alias=x86_64-unknown-linux-gnu
>> ac_cache_corrupted=false
>> ac_clean_files=
>> ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
>> ac_compiler_gnu=
>> ac_confdir=.
>> ac_config_commands=' default-1'
>> ac_config_guess='/bin/sh bin/config.guess'
>> ac_config_headers=' src/H5config.h'
>> ac_config_libobj_dir=.
>> ac_config_sub='/bin/sh bin/config.sub'
>> ac_configure='/bin/sh bin/configure'
>> ac_configure_args=' '\''--disable-shared'\''
>> '\''--prefix=/usr/local'\'' '\''--with-build-path=/usr/local'\''
>> '\''CFLAGS=${CFLAGS} -fpic'\'' '\''CPPFLAGS=${CPPFLAGS} -fpic'\''
>> '\''CXXFLAGS=${CXXFLAGS} -fpic'\'''
>> ac_cpp='$CPP $CPPFLAGS'
>> ac_cv_build=x86_64-unknown-linux-gnu
>> ac_cv_env_CC_set=
>> ac_cv_env_CC_value=
>> ac_cv_env_CFLAGS_set=set
>> ac_cv_env_CFLAGS_value='${CFLAGS} -fpic'
>> ac_cv_env_CPPFLAGS_set=set
>> ac_cv_env_CPPFLAGS_value='${CPPFLAGS} -fpic'
>> ac_cv_env_CPP_set=
>> ac_cv_env_CPP_value=
>> ac_cv_env_LDFLAGS_set=
>> ac_cv_env_LDFLAGS_value=
>> ac_cv_env_LIBS_set=
>> ac_cv_env_LIBS_value=
>> ac_cv_env_build_alias_set=
>> ac_cv_env_build_alias_value=
>> ac_cv_env_host_alias_set=
>> ac_cv_env_host_alias_value=
>> ac_cv_env_target_alias_set=
>> ac_cv_env_target_alias_value=
>> ac_cv_host=x86_64-unknown-linux-gnu
>> ac_dashdash=
>> ac_default_prefix=/usr/local/hdf5-1.6.6/hdf5
>> ac_dir=bin
>> ac_env_CC_set=
>> ac_env_CC_value=
>> ac_env_CFLAGS_set=set
>> ac_env_CFLAGS_value='${CFLAGS} -fpic'
>> ac_env_CPPFLAGS_set=set
>> ac_env_CPPFLAGS_value='${CPPFLAGS} -fpic'
>> ac_env_CPP_set=
>> ac_env_CPP_value=
>> ac_env_LDFLAGS_set=
>> ac_env_LDFLAGS_value=
>> ac_env_LIBS_set=
>> ac_env_LIBS_value=
>> ac_env_build_alias_set=
>> ac_env_build_alias_value=
>> ac_env_host_alias_set=
>> ac_env_host_alias_value=
>> ac_env_target_alias_set=
>> ac_env_target_alias_value=
>> ac_envvar=CXXFLAGS
>> ac_ext=c
>> ac_feature=shared
>> ac_hostname=localhost.localdomain
>> ac_includes_default='#include <stdio.h>
>> #ifdef HAVE_SYS_TYPES_H
>> # include <sys/types.h>
>> #endif
>> #ifdef HAVE_SYS_STAT_H
>> # include <sys/stat.h>
>> #endif
>> #ifdef STDC_HEADERS
>> # include <stdlib.h>
>> # include <stddef.h>
>> #else
>> # ifdef HAVE_STDLIB_H
>> #  include <stdlib.h>
>> # endif
>> #endif
>> #ifdef HAVE_STRING_H
>> # if !defined STDC_HEADERS && defined HAVE_MEMORY_H
>> #  include <memory.h>
>> # endif
>> # include <string.h>
>> #endif
>> #ifdef HAVE_STRINGS_H
>> # include <strings.h>
>> #endif
>> #ifdef HAVE_INTTYPES_H
>> # include <inttypes.h>
>> #endif
>> #ifdef HAVE_STDINT_H
>> # include <stdint.h>
>> #endif
>> #ifdef HAVE_UNISTD_H
>> # include <unistd.h>
>> #endif'
>> ac_init_help=
>> ac_init_version=false
>> ac_install_sh='bin/install-sh -c'
>> ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS
>> conftest.$ac_ext $LIBS >&5'
>> ac_ls_di='2613555 .'
>> ac_msg='sources are in ., but `cd .'\'' does not work'
>> ac_must_keep_next=false
>> ac_new_set=
>> ac_new_val=
>> ac_old_set=
>> ac_old_val=
>> ac_optarg='${CXXFLAGS} -fpic'
>> ac_option='CXXFLAGS=${CXXFLAGS} -fpic'
>> ac_package=build_path
>> ac_pass=2
>> ac_precious_vars='build_alias
>> host_alias
>> target_alias
>> CC
>> CFLAGS
>> LDFLAGS
>> LIBS
>> CPPFLAGS
>> CPP'
>> ac_prev=
>> ac_pwd=/usr/local/hdf5-1.6.6
>> ac_pwd_ls_di='2613555 .'
>> ac_save_IFS=' 	
>> '
>> ac_signal=0
>> ac_site_file=/usr/local/etc/config.site
>> ac_srcdir_defaulted=yes
>> ac_subdirs_all='${config_dirs}'
>> ac_subst_files='DEPEND
>> COMMENCE
>> CONCLUDE'
>> ac_subst_vars='SHELL
>> PATH_SEPARATOR
>> PACKAGE_NAME
>> PACKAGE_TARNAME
>> PACKAGE_VERSION
>> PACKAGE_STRING
>> PACKAGE_BUGREPORT
>> exec_prefix
>> prefix
>> program_transform_name
>> bindir
>> sbindir
>> libexecdir
>> datarootdir
>> datadir
>> sysconfdir
>> sharedstatedir
>> localstatedir
>> includedir
>> oldincludedir
>> docdir
>> infodir
>> htmldir
>> dvidir
>> pdfdir
>> psdir
>> libdir
>> localedir
>> mandir
>> DEFS
>> ECHO_C
>> ECHO_N
>> ECHO_T
>> LIBS
>> build_alias
>> host_alias
>> target_alias
>> build
>> build_cpu
>> build_vendor
>> build_os
>> host
>> host_cpu
>> host_vendor
>> host_os
>> CPPFLAGS
>> H5_CPPFLAGS
>> H5_CFLAGS
>> DEFAULT_LIBS
>> HSIZET
>> CC
>> CFLAGS
>> LDFLAGS
>> ac_ct_CC
>> EXEEXT
>> OBJEXT
>> config_dirs
>> subdirs
>> LT_STATIC_EXEC
>> PERL
>> AR
>> SET_MAKE
>> INSTALL_PROGRAM
>> INSTALL_SCRIPT
>> INSTALL_DATA
>> PARALLEL
>> RUNSERIAL
>> RUNPARALLEL
>> TESTPARALLEL
>> BUILD_PARALLEL_CONDITIONAL_TRUE
>> BUILD_PARALLEL_CONDITIONAL_FALSE
>> LN_S
>> ECHO
>> RANLIB
>> STRIP
>> CPP
>> GREP
>> EGREP
>> LIBTOOL
>> USE_FILTER_DEFLATE
>> USE_FILTER_SZIP
>> SSL
>> GASS
>> TESTGASS
>> 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
>>     
>
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>