1

This is the first time to install from source code in my life so thank you for any help.

I am trying to install h4toh5 utility which could allow converting a hdf4 to hdf5 file. After a long process of reading online, I figured out how to configure.

./configure CC=/usr/bin/h4cc --with-hdf5=/usr/lib/x86_64-linux-gnu --prefix=/home/cyue/Documents/tools

The installation instruction says I have to use the h4cc to compile: The HDF4 Library installs h4cc scripts which can replace cc. h4cc should be specified as the C Compiler. This can be done by passing the following to the configure script:

CC=<hdf4directory>/bin/h4cc                                              

At the beginning I don't have this but after installing HDF4-tools I confirm that I have /usr/bin/h4cc on my system. However, I am having final error like this:

    checking for a BSD-compatible install... /usr/bin/install -c
    checking whether build environment is sane... yes
    checking for a thread-safe mkdir -p... /bin/mkdir -p
    checking for gawk... gawk
    checking whether make sets $(MAKE)... yes
    checking whether to enable maintainer-specific portions of Makefiles... no
    checking for ranlib... ranlib
    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 for gcc... /usr/bin/h4cc
    checking whether the C compiler works... no
    configure: error: in `/home/cyue/Downloads/h4h5tools-2.2.2':
    configure: error: C compiler cannot create executables
    See `config.log' for more details.

The detailed config.log:

    This file contains any messages produced by compilers while
    running configure, to aid debugging if configure makes a mistake.

    It was created by H4H5Tools configure 2.2.2, which was
    generated by GNU Autoconf 2.65.  Invocation command line was

      $ ./configure CC=/usr/bin/h4cc --with-hdf5=/usr/lib/x86_64-linux-gnu --prefix=/home/cyue/Documents/tools

    ## --------- ##
    ## Platform. ##
    ## --------- ##

    hostname = LGGE130
    uname -m = x86_64
    uname -r = 3.16.0-4-amd64
    uname -s = Linux
    uname -v = #1 SMP Debian 3.16.7-ckt11-1+deb8u3 (2015-08-04)

    /usr/bin/uname -p = unknown
    /bin/uname -X     = unknown

    /bin/arch              = unknown
    /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/local/bin
    PATH: /usr/bin
    PATH: /bin
    PATH: /usr/local/games
    PATH: /usr/games
    PATH: /var/cfengine/bin


    ## ----------- ##
    ## Core tests. ##
    ## ----------- ##

    configure:2142: checking for a BSD-compatible install
    configure:2210: result: /usr/bin/install -c
    configure:2221: checking whether build environment is sane
    configure:2271: result: yes
    configure:2412: checking for a thread-safe mkdir -p
    configure:2451: result: /bin/mkdir -p
    configure:2464: checking for gawk
    configure:2480: found /usr/bin/gawk
    configure:2491: result: gawk
    configure:2502: checking whether make sets $(MAKE)
    configure:2524: result: yes
    configure:2605: checking whether to enable maintainer-specific portions of Makefiles
    configure:2614: result: no
    configure:2670: checking for ranlib
    configure:2686: found /usr/bin/ranlib
    configure:2697: result: ranlib
    configure:2724: checking build system type
    configure:2738: result: x86_64-unknown-linux-gnu
    configure:2758: checking host system type
    configure:2771: result: x86_64-unknown-linux-gnu
    configure:2794: checking shell variables initial values
    ACLOCAL='${SHELL} /home/cyue/Downloads/h4h5tools-2.2.2/bin/missing --run aclocal-1.11'
    AMTAR='${SHELL} /home/cyue/Downloads/h4h5tools-2.2.2/bin/missing --run tar'
    AUTOCONF='${SHELL} /home/cyue/Downloads/h4h5tools-2.2.2/bin/missing --run autoconf'
    AUTOHEADER='${SHELL} /home/cyue/Downloads/h4h5tools-2.2.2/bin/missing --run autoheader'
    AUTOMAKE='${SHELL} /home/cyue/Downloads/h4h5tools-2.2.2/bin/missing --run automake-1.11'
    AWK=gawk
    BASEDATADIR=homel/ychao/basedata
    BASH=/bin/bash
    BASHOPTS=cmdhist:complete_fullquote:extquote:force_fignore:hostcomplete:interactive_comments:progcomp:promptvars:sourcepath
    BASH_ALIASES=()
    BASH_ARGC=([0]="3")
    BASH_ARGV=([0]="--prefix=/home/cyue/Documents/tools" [1]="--with-hdf5=/usr/lib/x86_64-linux-gnu" [2]="CC=/usr/bin/h4cc")
    BASH_CMDS=()
    BASH_LINENO=([0]="0")
    BASH_SOURCE=([0]="./configure")
    BASH_VERSINFO=([0]="4" [1]="3" [2]="30" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu")
    BASH_VERSION='4.3.30(1)-release'
    CC=/usr/bin/h4cc
    CONFIG_SHELL=/bin/bash
    CYGPATH_W=echo
    DBUS_SESSION_BUS_ADDRESS=unix:abstract=/tmp/dbus-tC6gSQHljc,guid=5c6130f74e9fde0b455bfc4555ce3181
    DESKTOP_SESSION=default
    DIRSTACK=()
    DISPLAY=:0
    DUALCASE=1
    ECHO_C=
    ECHO_N=-n
    ECHO_T=
    EUID=7277
    FER_DATA='. /data /usr/local/ferret//go /usr/local/ferret//examples /usr/local/ferret//contrib /data/ncep'
    FER_DESCR='. /descr'
    FER_DIR=/usr/local/ferret/
    FER_EXTERNAL_FUNCTIONS=/usr/local/ferret//ext_func/libs
    FER_GO='. /usr/local/ferret//go /usr/local/ferret//examples /usr/local/ferret//contrib'
    FER_GRIDS='. /grids'
    FER_PALETTE='. /usr/local/ferret//ppl'
    FER_PATHS=/usr/local/ferret_paths
    GDMSESSION=default
    GDM_LANG=en_US.utf8
    GJS_DEBUG_OUTPUT=stderr
    GJS_DEBUG_TOPICS='JS ERROR;JS LOG'
    GNOME_DESKTOP_SESSION_ID=this-is-deprecated
    GPG_AGENT_INFO=/run/user/7277/keyring/gpg:0:1
    GROUPS=()
    GTK_IM_MODULE=ibus
    HOME=/home/cyue
    HOSTNAME=LGGE130
    HOSTTYPE=x86_64
    IFS='   
    '
    INSTALL='/usr/bin/install -c'
    INSTALL_DATA='${INSTALL} -m 644'
    INSTALL_PROGRAM='${INSTALL}'
    INSTALL_SCRIPT='${INSTALL}'
    INSTALL_STRIP_PROGRAM='$(install_sh) -c -s'
    LANG=en_US.utf8
    LANGUAGE=C
    LC_ALL=C
    LIBOBJS=
    LINENO=2794
    LOADEDMODULES=
    LOGNAME=cyue
    LS_COLORS='rs=0:di=01;34:ln=01;36:mh=00:pi=40;33:so=01;35:do=01;35:bd=40;33;01:cd=40;33;01:or=40;31;01:su=37;41:sg=30;43:ca=30;41:tw=30;42:ow=34;42:st=37;44:ex=01;32:*.tar=01;31:*.tgz=01;31:*.arc=01;31:*.arj=01;31:*.taz=01;31:*.lha=01;31:*.lz4=01;31:*.lzh=01;31:*.lzma=01;31:*.tlz=01;31:*.txz=01;31:*.tzo=01;31:*.t7z=01;31:*.zip=01;31:*.z=01;31:*.Z=01;31:*.dz=01;31:*.gz=01;31:*.lrz=01;31:*.lz=01;31:*.lzo=01;31:*.xz=01;31:*.bz2=01;31:*.bz=01;31:*.tbz=01;31:*.tbz2=01;31:*.tz=01;31:*.deb=01;31:*.rpm=01;31:*.jar=01;31:*.war=01;31:*.ear=01;31:*.sar=01;31:*.rar=01;31:*.alz=01;31:*.ace=01;31:*.zoo=01;31:*.cpio=01;31:*.7z=01;31:*.rz=01;31:*.cab=01;31:*.jpg=01;35:*.jpeg=01;35:*.gif=01;35:*.bmp=01;35:*.pbm=01;35:*.pgm=01;35:*.ppm=01;35:*.tga=01;35:*.xbm=01;35:*.xpm=01;35:*.tif=01;35:*.tiff=01;35:*.png=01;35:*.svg=01;35:*.svgz=01;35:*.mng=01;35:*.pcx=01;35:*.mov=01;35:*.mpg=01;35:*.mpeg=01;35:*.m2v=01;35:*.mkv=01;35:*.webm=01;35:*.ogm=01;35:*.mp4=01;35:*.m4v=01;35:*.mp4v=01;35:*.vob=01;35:*.qt=01;35:*.nuv=01;35:*.wmv=01;35:*.asf=01;35:*.rm=01;35:*.rmvb=01;35:*.flc=01;35:*.avi=01;35:*.fli=01;35:*.flv=01;35:*.gl=01;35:*.dl=01;35:*.xcf=01;35:*.xwd=01;35:*.yuv=01;35:*.cgm=01;35:*.emf=01;35:*.axv=01;35:*.anx=01;35:*.ogv=01;35:*.ogx=01;35:*.aac=00;36:*.au=00;36:*.flac=00;36:*.m4a=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:*.axa=00;36:*.oga=00;36:*.spx=00;36:*.xspf=00;36:'
    MACHTYPE=x86_64-pc-linux-gnu
    MAINT='#'
    MAINTAINER_MODE_FALSE=
    MAINTAINER_MODE_TRUE='#'
    MAKEFLAGS=
    MAKEINFO='${SHELL} /home/cyue/Downloads/h4h5tools-2.2.2/bin/missing --run makeinfo'
    MANPATH=:/var/cfengine/share/man
    MFLAGS=
    MISSING='${SHELL} /home/cyue/Downloads/h4h5tools-2.2.2/bin/missing'
    MKDIR_P='/bin/mkdir -p'
    MODULEPATH='/etc/environment-modules/modules:/usr/share/modules/versions:/usr/Modules/$MODULE_VERSION/modulefiles:/usr/share/modules/modulefiles'
    MODULESHOME=/usr/share/modules
    MODULE_VERSION=3.2.10
    MODULE_VERSION_STACK=3.2.10
    OPTERR=1
    OPTIND=1
    OSTYPE=linux-gnu
    PACKAGE=h4h5tools
    PACKAGE_BUGREPORT=help@hdfgroup.org
    PACKAGE_NAME=H4H5Tools
    PACKAGE_STRING='H4H5Tools 2.2.2'
    PACKAGE_TARNAME=h4h5tools
    PACKAGE_URL=
    PACKAGE_VERSION=2.2.2
    PATH=/usr/local/bin:/usr/bin:/bin:/usr/local/games:/usr/games:/var/cfengine/bin
    PATH_SEPARATOR=:
    PIPESTATUS=([0]="0")
    PLOTFONTS=/usr/local/ferret//ppl/fonts
    POSIXLY_CORRECT=y
    PPID=4806
    PS1='$ '
    PS2='> '
    PS4='+ '
    PWD=/home/cyue/Downloads/h4h5tools-2.2.2
    PYDIR=/home/cyue/python/
    PYTHONPATH=/home/cyue/python/pylsce:/home/cyue/python/libstudy
    QT_IM_MODULE=ibus
    RANLIB=ranlib
    SESSION_MANAGER=local/LGGE130:@/tmp/.ICE-unix/1687,unix/LGGE130:/tmp/.ICE-unix/1687
    SET_MAKE=
    SHELL=/bin/bash
    SHELLOPTS=braceexpand:hashall:interactive-comments:posix
    SHLVL=2
    SPECTRA=/usr/local/ferret//ppl
    SSH_AGENT_PID=1727
    SSH_AUTH_SOCK=/run/user/7277/keyring/ssh
    TERM=xterm
    TMAP=/usr/local/ferret//fmt
    UID=7277
    USER=cyue
    USERNAME=cyue
    USE_MAINTAINER_MODE=no
    VERSION=2.2.2
    VTE_VERSION=3801
    WINDOWID=31457286
    WINDOWPATH=7
    XAUTHORITY=/var/run/gdm3/auth-for-cyue-BlQ3QV/database
    XDG_CURRENT_DESKTOP=GNOME
    XDG_DATA_DIRS=/usr/share/gnome:/usr/local/share/:/usr/share/
    XDG_MENU_PREFIX=gnome-
    XDG_RUNTIME_DIR=/run/user/7277
    XDG_SEAT=seat0
    XDG_SESSION_DESKTOP=default
    XDG_SESSION_ID=1
    XDG_VTNR=7
    XMODIFIERS=@im=ibus
    _='checking shell variables initial values... '
    ac_abs_confdir=/home/cyue/Downloads/h4h5tools-2.2.2
    ac_arg=CC=/usr/bin/h4cc
    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_guess='/bin/bash bin/config.guess'
    ac_config_libobj_dir=.
    ac_config_sub='/bin/bash bin/config.sub'
    ac_configure='/bin/bash bin/configure'
    ac_configure_args=' '\''CC=/usr/bin/h4cc'\'' '\''--with-hdf5=/usr/lib/x86_64-linux-gnu'\'' '\''--prefix=/home/cyue/Documents/tools'\'''
    ac_cpp='$CPP $CPPFLAGS'
    ac_ct_RANLIB=ranlib
    ac_cv_build=x86_64-unknown-linux-gnu
    ac_cv_env_CC_set=set
    ac_cv_env_CC_value=/usr/bin/h4cc
    ac_cv_env_CFLAGS_set=
    ac_cv_env_CFLAGS_value=
    ac_cv_env_CPPFLAGS_set=
    ac_cv_env_CPPFLAGS_value=
    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_path_install='/usr/bin/install -c'
    ac_cv_path_mkdir=/bin/mkdir
    ac_cv_prog_AWK=gawk
    ac_cv_prog_ac_ct_RANLIB=ranlib
    ac_cv_prog_make_make_set=yes
    ac_dashdash=
    ac_default_prefix=/usr/local
    ac_dir=bin
    ac_env_CC_set=set
    ac_env_CC_value=/usr/bin/h4cc
    ac_env_CFLAGS_set=
    ac_env_CFLAGS_value=
    ac_env_CPPFLAGS_set=
    ac_env_CPPFLAGS_value=
    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=CC
    ac_exec_ext=
    oldincludedir
    includedir
    localstatedir
    sharedstatedir
    sysconfdir
    datadir
    datarootdir
    libexecdir
    sbindir
    bindir
    program_transform_name
    prefix
    exec_prefix
    PACKAGE_URL
    PACKAGE_BUGREPORT
    PACKAGE_STRING
    PACKAGE_VERSION
    PACKAGE_TARNAME
    PACKAGE_NAME
    PATH_SEPARATOR
    SHELL'
    ac_t=install-sh
    ac_tool_prefix=
    ac_unique_file=lib/src/h4toh5main.c
    ac_unrecognized_opts=
    ac_unrecognized_sep=
    ac_user_opts='
    enable_option_checking
    enable_maintainer_mode
    enable_dependency_tracking
    enable_static_exec
    with_fnord
    with_hdf5
    with_hdfeos2
    enable_production
    '
    ac_useropt=hdf5
    ac_useropt_orig=hdf5
    ac_val='${datarootdir}/man'
    ac_var=CPP
    ac_word=ranlib
    am__api_version=1.11
    am__leading_dot=.
    am__tar='${AMTAR} chof - "$$tardir"'
    am__untar='${AMTAR} xf -'
    am_aux_dir=/home/cyue/Downloads/h4h5tools-2.2.2/bin
    am_lf='
    '
    am_missing_run='${SHELL} /home/cyue/Downloads/h4h5tools-2.2.2/bin/missing --run '
    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/bin
    as_dirname=dirname
    as_echo='printf %s\n'
    as_echo_n='printf %s'
    as_executable_p='test -x'
    as_expr=expr
    as_lineno_1=425
    as_lineno_1a=425
    as_lineno_2=426
    as_lineno_2a=426
    as_ln_s='ln -s'
    as_me=configure
    as_mkdir_p='mkdir -p "$as_dir"'
    as_myself=./configure
    as_nl='
    '
    as_save_IFS='   
    '
    as_test_x='test -x'
    as_tr_cpp='eval sed '\''y%*abcdefghijklmnopqrstuvwxyz%PABCDEFGHIJKLMNOPQRSTUVWXYZ%;s%[^_abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ0123456789]%_%g'\'''
    as_tr_sh='eval sed '\''y%*+%pp%;s%[^_abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ0123456789]%_%g'\'''
    as_unset=as_fn_unset
    as_var=ac_cv_prog_make_make_set
    bindir='${exec_prefix}/bin'
    build=x86_64-unknown-linux-gnu
    build_cpu=x86_64
    build_os=linux-gnu
    build_vendor=unknown
    cache_file=/dev/null
    cross_compiling=no
    datadir='${datarootdir}'
    datarootdir='${prefix}/share'
    docdir='${datarootdir}/doc/${PACKAGE_TARNAME}'
    dvidir='${docdir}'
    exec_prefix=NONE
    host=x86_64-unknown-linux-gnu
    host_cpu=x86_64
    host_os=linux-gnu
    host_vendor=unknown
    htmldir='${docdir}'
    includedir='${prefix}/include'
    infodir='${datarootdir}/info'
    install_sh='${SHELL} /home/cyue/Downloads/h4h5tools-2.2.2/bin/install-sh'
    libdir='${exec_prefix}/lib'
    libexecdir='${exec_prefix}/libexec'
    localedir='${datarootdir}/locale'
    localstatedir='${prefix}/var'
    mandir='${datarootdir}/man'
    mkdir_p='/bin/mkdir -p'
    no_create=
    no_recursion=
    oldincludedir=/usr/include
    pdfdir='${docdir}'
    prefix=/home/cyue/Documents/tools
    program_prefix=NONE
    program_suffix=NONE
    program_transform_name=s,x,x,
    psdir='${docdir}'
    pylibast=/ahome/python/python_lib
    sbindir='${exec_prefix}/sbin'
    sharedstatedir='${prefix}/com'
    silent=
    site=
    srcdir=.
    subdirs=
    sysconfdir='${prefix}/etc'
    target=
    verbose=
    with_hdf5=/usr/lib/x86_64-linux-gnu
    x_includes=NONE
    x_libraries=NONE
    configure:2797: result: done
    configure:2848: checking for gcc
    configure:2875: result: /usr/bin/h4cc
    configure:3104: checking for C compiler version
    configure:3113: /usr/bin/h4cc --version >&5
    gcc (Debian 4.9.2-10) 4.9.2
    Copyright (C) 2014 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.

    gcc: error: /usr/lib/libmfhdf.a: No such file or directory
    gcc: error: /usr/lib/libdf.a: No such file or directory
    configure:3124: $? = 0
    configure:3113: /usr/bin/h4cc -v >&5
    gcc: error: /usr/lib/libmfhdf.a: No such file or directory
    gcc: error: /usr/lib/libdf.a: No such file or directory
    Using built-in specs.
    COLLECT_GCC=gcc
    COLLECT_LTO_WRAPPER=/usr/lib/gcc/x86_64-linux-gnu/4.9/lto-wrapper
    Target: x86_64-linux-gnu
    Configured with: ../src/configure -v --with-pkgversion='Debian 4.9.2-10' --with-bugurl=file:///usr/share/doc/gcc-4.9/README.Bugs --enable-languages=c,c++,java,go,d,fortran,objc,obj-c++ --prefix=/usr --program-suffix=-4.9 --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --with-gxx-include-dir=/usr/include/c++/4.9 --libdir=/usr/lib --enable-nls --with-sysroot=/ --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --enable-gnu-unique-object --disable-vtable-verify --enable-plugin --with-system-zlib --disable-browser-plugin --enable-java-awt=gtk --enable-gtk-cairo --with-java-home=/usr/lib/jvm/java-1.5.0-gcj-4.9-amd64/jre --enable-java-home --with-jvm-root-dir=/usr/lib/jvm/java-1.5.0-gcj-4.9-amd64 --with-jvm-jar-dir=/usr/lib/jvm-exports/java-1.5.0-gcj-4.9-amd64 --with-arch-directory=amd64 --with-ecj-jar=/usr/share/java/eclipse-ecj.jar --enable-objc-gc --enable-multiarch --with-arch-32=i586 --with-abi=m64 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu
    Thread model: posix
    gcc version 4.9.2 (Debian 4.9.2-10) 
    configure:3124: $? = 1
    configure:3113: /usr/bin/h4cc -V >&5
    gcc: error: /usr/lib/libmfhdf.a: No such file or directory
    gcc: error: /usr/lib/libdf.a: No such file or directory
    gcc: error: unrecognized command line option '-V'
    configure:3124: $? = 1
    configure:3113: /usr/bin/h4cc -qversion >&5
    gcc: error: /usr/lib/libmfhdf.a: No such file or directory
    gcc: error: /usr/lib/libdf.a: No such file or directory
    gcc: error: unrecognized command line option '-qversion'
    configure:3124: $? = 1
    configure:3144: checking whether the C compiler works
    configure:3166: /usr/bin/h4cc    conftest.c  >&5
    gcc: error: /usr/lib/libmfhdf.a: No such file or directory
    gcc: error: /usr/lib/libdf.a: No such file or directory
    configure:3170: $? = 1
    configure:3208: result: no
    configure: failed program was:
    | /* confdefs.h */
    | #define PACKAGE_NAME "H4H5Tools"
    | #define PACKAGE_TARNAME "h4h5tools"
    | #define PACKAGE_VERSION "2.2.2"
    | #define PACKAGE_STRING "H4H5Tools 2.2.2"
    | #define PACKAGE_BUGREPORT "help@hdfgroup.org"
    | #define PACKAGE_URL ""
    | #define PACKAGE "h4h5tools"
    | #define VERSION "2.2.2"
    | /* end confdefs.h.  */
    | 
    | int
    | main ()
    | {
    | 
    |   ;
    |   return 0;
    | }
    configure:3213: error: in `/home/cyue/Downloads/h4h5tools-2.2.2':
    configure:3217: 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=set
    ac_cv_env_CC_value=/usr/bin/h4cc
    ac_cv_env_CFLAGS_set=
    ac_cv_env_CFLAGS_value=
    ac_cv_env_CPPFLAGS_set=
    ac_cv_env_CPPFLAGS_value=
    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_path_install='/usr/bin/install -c'
    ac_cv_path_mkdir=/bin/mkdir
    ac_cv_prog_AWK=gawk
    ac_cv_prog_ac_ct_CC=/usr/bin/h4cc
    ac_cv_prog_ac_ct_RANLIB=ranlib
    ac_cv_prog_make_make_set=yes

    ## ----------------- ##
    ## Output variables. ##
    ## ----------------- ##

    ACLOCAL='${SHELL} /home/cyue/Downloads/h4h5tools-2.2.2/bin/missing --run aclocal-1.11'
    AMDEPBACKSLASH=''
    AMDEP_FALSE=''
    AMDEP_TRUE=''
    AMTAR='${SHELL} /home/cyue/Downloads/h4h5tools-2.2.2/bin/missing --run tar'
    AR=''
    AUTOCONF='${SHELL} /home/cyue/Downloads/h4h5tools-2.2.2/bin/missing --run autoconf'
    AUTOHEADER='${SHELL} /home/cyue/Downloads/h4h5tools-2.2.2/bin/missing --run autoheader'
    AUTOMAKE='${SHELL} /home/cyue/Downloads/h4h5tools-2.2.2/bin/missing --run automake-1.11'
    AWK='gawk'
    CC='/usr/bin/h4cc'
    CCDEPMODE=''
    CFLAGS=''
    CPP=''
    CPPFLAGS=''
    CYGPATH_W='echo'
    DEFS=''
    DEPDIR=''
    ECHO_C=''
    ECHO_N='-n'
    ECHO_T=''
    EGREP=''
    EXEEXT=''
    GREP=''
    H4_USE_FILTER_SZIP=''
    H5_USE_FILTER_SZIP=''
    H5_USE_FILTER_ZLIB=''
    H5_USE_HDFEOS2=''
    H5_USE_SZIP_ENCODER=''
    HDF5PATH=''
    INSTALL_DATA='${INSTALL} -m 644'
    INSTALL_PROGRAM='${INSTALL}'
    INSTALL_SCRIPT='${INSTALL}'
    INSTALL_STRIP_PROGRAM='$(install_sh) -c -s'
    LDFLAGS=''
    LD_LIBRARY_PATH=''
    LIBHDF5=''
    LIBOBJS=''
    LIBS=''
    LTLIBOBJS=''
    LT_STATIC_EXEC=''
    MAINT='#'
    MAINTAINER_MODE_FALSE=''
    MAINTAINER_MODE_TRUE='#'
    MAKEINFO='${SHELL} /home/cyue/Downloads/h4h5tools-2.2.2/bin/missing --run makeinfo'
    MKDIR_P='/bin/mkdir -p'
    OBJEXT=''
    PACKAGE='h4h5tools'
    PACKAGE_BUGREPORT='help@hdfgroup.org'
    PACKAGE_NAME='H4H5Tools'
    PACKAGE_STRING='H4H5Tools 2.2.2'
    PACKAGE_TARNAME='h4h5tools'
    PACKAGE_URL=''
    PACKAGE_VERSION='2.2.2'
    PARALLEL=''
    PATH_SEPARATOR=':'
    PERL=''
    RANLIB='ranlib'
    RUNPARALLEL=''
    RUNSERIAL=''
    SEARCH=''
    SETX=''
    SET_MAKE=''
    SHELL='/bin/bash'
    STRIP=''
    TESTPARALLEL=''
    VERSION='2.2.2'
    ac_ct_CC='/usr/bin/h4cc'
    am__EXEEXT_FALSE=''
    am__EXEEXT_TRUE=''
    am__fastdepCC_FALSE=''
    am__fastdepCC_TRUE=''
    am__include=''
    am__isrc=''
    am__leading_dot='.'
    am__quote=''
    am__tar='${AMTAR} chof - "$$tardir"'
    am__untar='${AMTAR} xf -'
    bindir='${exec_prefix}/bin'
    build='x86_64-unknown-linux-gnu'
    build_alias=''
    build_cpu='x86_64'
    build_os='linux-gnu'
    build_vendor='unknown'
    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'
    install_sh='${SHELL} /home/cyue/Downloads/h4h5tools-2.2.2/bin/install-sh'
    libdir='${exec_prefix}/lib'
    libexecdir='${exec_prefix}/libexec'
    localedir='${datarootdir}/locale'
    localstatedir='${prefix}/var'
    mandir='${datarootdir}/man'
    mkdir_p='/bin/mkdir -p'
    oldincludedir='/usr/include'
    pdfdir='${docdir}'
    prefix='/home/cyue/Documents/tools'
    program_transform_name='s,x,x,'
    psdir='${docdir}'
    sbindir='${exec_prefix}/sbin'
    sharedstatedir='${prefix}/com'
    sysconfdir='${prefix}/etc'
    target_alias=''

    ## ------------------- ##
    ## File substitutions. ##
    ## ------------------- ##

    COMMENCE=''
    CONCLUDE=''
    DEPEND=''

    ## ----------- ##
    ## confdefs.h. ##
    ## ----------- ##

    /* confdefs.h */
    #define PACKAGE_NAME "H4H5Tools"
    #define PACKAGE_TARNAME "h4h5tools"
    #define PACKAGE_VERSION "2.2.2"
    #define PACKAGE_STRING "H4H5Tools 2.2.2"
    #define PACKAGE_BUGREPORT "help@hdfgroup.org"
    #define PACKAGE_URL ""
    #define PACKAGE "h4h5tools"
    #define VERSION "2.2.2"

    configure: exit 77

However I did try to compile using gcc a hello.c and it works fine. Could anyone give me some hints? Thank you in advance !!

  • gcc happily compiles a hello.c. but does h4cc work ? checking for gcc... /usr/bin/h4cc – steve Aug 15 '15 at 16:00
  • Why does the C Compiler line point to h4cc? checking for gcc... /usr/bin/h4cc = hdf4-tools, so try sudo apt get install hdf4-tools before compiling, or remove --with-hdf5. See Search Results – eyoung100 Aug 15 '15 at 17:57
  • @steve, sorry, I don't know what you mean by "checking for gcc... /usr/bin/h4cc? " h4cc is the recommended compiler shipped with HDF4-tools, but anyway, following the suggestions by steeldriver (as below), at least this error disappeared and I am having another error. – wiswit Aug 15 '15 at 18:47
  • @eyoung100, I installed hdf4-tools before compiling, as only by this I am having h4cc. But why need to remove --with-hdf5? as this is recommend in the installation instruction. – wiswit Aug 15 '15 at 18:48
  • Have you rebooted since installing? As Perror points out your system cannot find the hdf4-tools. Logging Out/rebooting Will fix this. What is the result of which h4cc? – eyoung100 Aug 15 '15 at 19:03
5

According to your log file, you are missing the libmfhdf.a and libdf.a static libraries. Here is the interesting part of the log:

gcc: error: /usr/lib/libmfhdf.a: No such file or directory
gcc: error: /usr/lib/libdf.a: No such file or directory
configure:3124: $? = 0
configure:3113: /usr/bin/h4cc -v >&5
gcc: error: /usr/lib/libmfhdf.a: No such file or directory
gcc: error: /usr/lib/libdf.a: No such file or directory

Try to locate in which package you can get it and install it.

  • 2
    ... probably libhdf4-dev if you are using a Debian-based distribution – steeldriver Aug 15 '15 at 16:03
  • I agree with steeldriver, this should be the package to get it to make it work. – perror Aug 15 '15 at 16:04
  • 1
    @steeldriver perror , you two are right. I checked all hdf4 related libraries I am having and none of them contain the files requested. So I installed libhdf4-dev and verified that the request files are there. Now the original error disappeared and was replaced with a new one: error: cannot find HDF5 header files! I guess I have to again install libhdf5-dev, BTW, could you briefly explain why we need "development" versions? as briefly mentioned at the end of here: control-escape.com/linux/lx-swinstall-tar.html. Thx. – wiswit Aug 15 '15 at 18:58
  • If the previous error disapeared, then close this question by marking the correct answer and start a new question. And, you need the development version because you are compiling against this library, so you are "developing". – perror Aug 15 '15 at 19:12

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service, privacy policy and cookie policy

Not the answer you're looking for? Browse other questions tagged or ask your own question.