UnclePutin UnclePutin - 3 months ago 17
C Question

HDF-EOS configure fails, "C compiler cannot create executables"

I am trying to install the HDF-EOS C library by using ./configure and during the execution of configure, I get this output:

./configure CC=/usr/local/hdf-4.2.12-linux-centos7-x86_64/bin/h4cc
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for gawk... no
checking for mawk... mawk
checking whether make sets $(MAKE)... yes
checking whether to enable maintainer-specific portions of Makefiles... no
checking build system type... x86_64-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
checking for style of include used by make... GNU
checking for gcc... /usr/local/hdf-4.2.12-linux-centos7-x86_64/bin/h4cc
checking for C compiler default output file name...
configure: error: C compiler cannot create executables
See `config.log' for more details.


The config.log is:

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

It was created by hdf-eos2 configure 4.2, which was
generated by GNU Autoconf 2.61. Invocation command line was

$ ./configure CC=/usr/local/hdf-4.2.12-linux-centos7-x86_64/bin/h4cc

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

hostname = kali
uname -m = x86_64
uname -r = 4.3.0-kali1-amd64
uname -s = Linux
uname -v = #1 SMP Debian 4.3.3-5kali4 (2016-01-13)

/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/sbin
PATH: /usr/local/bin
PATH: /usr/sbin
PATH: /usr/bin
PATH: /sbin
PATH: /bin
PATH: /usr/local/hdf5/bin
PATH: /usr/local/hdf4-4.2.12/bin
PATH: /usr/local/hdf5/bin
PATH: /usr/local/hdf4-4.2.12/bin
PATH: /usr/local/hdf-4.2.12-linux-centos7-x86_64/bin/h4cc
PATH: /usr/local/hdf5/bin


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

configure:2022: checking for a BSD-compatible install
configure:2078: result: /usr/bin/install -c
configure:2089: checking whether build environment is sane
configure:2132: result: yes
configure:2197: checking for gawk
configure:2227: result: no
configure:2197: checking for mawk
configure:2213: found /usr/bin/mawk
configure:2224: result: mawk
configure:2235: checking whether make sets $(MAKE)
configure:2256: result: yes
configure:2440: checking whether to enable maintainer-specific portions of Makefiles
configure:2449: result: no
configure:2546: checking build system type
configure:2564: result: x86_64-unknown-linux-gnu
configure:2586: checking host system type
configure:2601: result: x86_64-unknown-linux-gnu
configure:2635: checking for style of include used by make
configure:2663: result: GNU
configure:2736: checking for gcc
configure:2763: result: /usr/local/hdf-4.2.12-linux-centos7-x86_64/bin/h4cc
configure:3001: checking for C compiler version
configure:3008: /usr/local/hdf-4.2.12-linux-centos7-x86_64/bin/h4cc --version >&5
gcc: error: /mnt/scr1/pre-release/hdf4/v4.2.12/thg-builds/moohan-static/lib/libmfhdf.a: No such file or directory
gcc: error: /mnt/scr1/pre-release/hdf4/v4.2.12/thg-builds/moohan-static/lib/libdf.a: No such file or directory
gcc (Debian 6.1.1-11) 6.1.1 20160802
Copyright (C) 2016 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:3011: $? = 0
configure:3018: /usr/local/hdf-4.2.12-linux-centos7-x86_64/bin/h4cc -v >&5
gcc: error: /mnt/scr1/pre-release/hdf4/v4.2.12/thg-builds/moohan-static/lib/libmfhdf.a: No such file or directory
gcc: error: /mnt/scr1/pre-release/hdf4/v4.2.12/thg-builds/moohan-static/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/6/lto-wrapper
Target: x86_64-linux-gnu
Configured with: ../src/configure -v --with-pkgversion='Debian 6.1.1-11' --with-bugurl=file:///usr/share/doc/gcc-6/README.Bugs --enable-languages=c,ada,c++,java,go,d,fortran,objc,obj-c++ --prefix=/usr --program-suffix=-6 --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --with-sysroot=/ --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-vtable-verify --enable-libmpx --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-6-amd64/jre --enable-java-home --with-jvm-root-dir=/usr/lib/jvm/java-1.5.0-gcj-6-amd64 --with-jvm-jar-dir=/usr/lib/jvm-exports/java-1.5.0-gcj-6-amd64 --with-arch-directory=amd64 --with-ecj-jar=/usr/share/java/eclipse-ecj.jar --enable-objc-gc --enable-multiarch --with-arch-32=i686 --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 6.1.1 20160802 (Debian 6.1.1-11)
configure:3021: $? = 1
configure:3028: /usr/local/hdf-4.2.12-linux-centos7-x86_64/bin/h4cc -V >&5
gcc: error: /mnt/scr1/pre-release/hdf4/v4.2.12/thg-builds/moohan-static/lib/libmfhdf.a: No such file or directory
gcc: error: /mnt/scr1/pre-release/hdf4/v4.2.12/thg-builds/moohan-static/lib/libdf.a: No such file or directory
gcc: error: unrecognized command line option '-V'
configure:3031: $? = 1
configure:3054: checking for C compiler default output file name
configure:3081: /usr/local/hdf-4.2.12-linux-centos7-x86_64/bin/h4cc conftest.c >&5
gcc: error: /mnt/scr1/pre-release/hdf4/v4.2.12/thg-builds/moohan-static/lib/libmfhdf.a: No such file or directory
gcc: error: /mnt/scr1/pre-release/hdf4/v4.2.12/thg-builds/moohan-static/lib/libdf.a: No such file or directory
configure:3084: $? = 1
configure:3122: result:
configure: failed program was:
| /* confdefs.h. */
| #define PACKAGE_NAME "hdf-eos2"
| #define PACKAGE_TARNAME "hdf-eos2"
| #define PACKAGE_VERSION "4.2"
| #define PACKAGE_STRING "hdf-eos2 4.2"
| #define PACKAGE_BUGREPORT "null@bogus.email"
| #define PACKAGE "hdf-eos2"
| #define VERSION "4.2"
| /* end confdefs.h. */
|
| int
| main ()
| {
|
| ;
| return 0;
| }
configure:3129: 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_CCC_set=
ac_cv_env_CCC_value=
ac_cv_env_CC_set=set
ac_cv_env_CC_value=/usr/local/hdf-4.2.12-linux-centos7-x86_64/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_CXXCPP_set=
ac_cv_env_CXXCPP_value=
ac_cv_env_CXXFLAGS_set=
ac_cv_env_CXXFLAGS_value=
ac_cv_env_CXX_set=
ac_cv_env_CXX_value=
ac_cv_env_F77_set=
ac_cv_env_F77_value=
ac_cv_env_FCFLAGS_set=
ac_cv_env_FCFLAGS_value=
ac_cv_env_FC_set=
ac_cv_env_FC_value=
ac_cv_env_FFLAGS_set=
ac_cv_env_FFLAGS_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_prog_AWK=mawk
ac_cv_prog_ac_ct_CC=/usr/local/hdf-4.2.12-linux-centos7-x86_64/bin/h4cc
ac_cv_prog_make_make_set=yes

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

ACLOCAL='${SHELL} /usr/local/hdfeos/config/missing --run aclocal-1.9'
AMDEPBACKSLASH='\'
AMDEP_FALSE='#'
AMDEP_TRUE=''
AMTAR='${SHELL} /usr/local/hdfeos/config/missing --run tar'
AR=''
AUTOCONF='${SHELL} /usr/local/hdfeos/config/missing --run autoconf'
AUTOHEADER='${SHELL} /usr/local/hdfeos/config/missing --run autoheader'
AUTOMAKE='${SHELL} /usr/local/hdfeos/config/missing --run automake-1.9'
AWK='mawk'
CC='/usr/local/hdf-4.2.12-linux-centos7-x86_64/bin/h4cc'
CCDEPMODE=''
CFLAGS=''
CPP=''
CPPFLAGS=''
CXX=''
CXXCPP=''
CXXDEPMODE=''
CXXFLAGS=''
CYGPATH_W='echo'
DEFS=''
DEPDIR='.deps'
ECHO='echo'
ECHO_C=''
ECHO_N='-n'
ECHO_T=''
EGREP=''
EXEEXT=''
F2CFORTRAN_32PTR_CONDITIONAL_FALSE=''
F2CFORTRAN_32PTR_CONDITIONAL_TRUE=''
F2CFORTRAN_90_CONDITIONAL_FALSE=''
F2CFORTRAN_90_CONDITIONAL_TRUE=''
F2CFORTRAN_CONDITIONAL_FALSE=''
F2CFORTRAN_CONDITIONAL_TRUE=''
F77=''
FC=''
FCFLAGS=''
FFLAGS=''
GREP=''
INSTALL_DATA='${INSTALL} -m 644'
INSTALL_INCLUDE_CONDITIONAL_FALSE=''
INSTALL_INCLUDE_CONDITIONAL_TRUE=''
INSTALL_PROGRAM='${INSTALL}'
INSTALL_SCRIPT='${INSTALL}'
INSTALL_STRIP_PROGRAM='${SHELL} $(install_sh) -c -s'
LDFLAGS=''
LIBOBJS=''
LIBS=''
LIBTOOL=''
LN_S=''
LTLIBOBJS=''
MAINT='#'
MAINTAINER_MODE_FALSE=''
MAINTAINER_MODE_TRUE='#'
MAKEINFO='${SHELL} /usr/local/hdfeos/config/missing --run makeinfo'
OBJEXT=''
PACKAGE='hdf-eos2'
PACKAGE_BUGREPORT='null@bogus.email'
PACKAGE_NAME='hdf-eos2'
PACKAGE_STRING='hdf-eos2 4.2'
PACKAGE_TARNAME='hdf-eos2'
PACKAGE_VERSION='4.2'
PATH_SEPARATOR=':'
RANLIB=''
SET_MAKE=''
SHELL='/bin/bash'
STRIP=''
SZIP_ENCODER_CONDITIONAL_FALSE=''
SZIP_ENCODER_CONDITIONAL_TRUE=''
TESTDRIVERS_CONDITIONAL_FALSE=''
TESTDRIVERS_CONDITIONAL_TRUE=''
VERSION='4.2'
ac_ct_CC='/usr/local/hdf-4.2.12-linux-centos7-x86_64/bin/h4cc'
ac_ct_CXX=''
ac_ct_F77=''
ac_ct_FC=''
am__fastdepCC_FALSE=''
am__fastdepCC_TRUE=''
am__fastdepCXX_FALSE=''
am__fastdepCXX_TRUE=''
am__include='include'
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='/usr/local/hdfeos/config/install-sh'
libdir='${exec_prefix}/lib'
libexecdir='${exec_prefix}/libexec'
localedir='${datarootdir}/locale'
localstatedir='${prefix}/var'
mandir='${datarootdir}/man'
mkdir_p='mkdir -p --'
oldincludedir='/usr/include'
pdfdir='${docdir}'
prefix='NONE'
program_transform_name='s,x,x,'
psdir='${docdir}'
sbindir='${exec_prefix}/sbin'
sharedstatedir='${prefix}/com'
sysconfdir='${prefix}/etc'
target_alias=''

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

#define PACKAGE_NAME "hdf-eos2"
#define PACKAGE_TARNAME "hdf-eos2"
#define PACKAGE_VERSION "4.2"
#define PACKAGE_STRING "hdf-eos2 4.2"
#define PACKAGE_BUGREPORT "null@bogus.email"
#define PACKAGE "hdf-eos2"
#define VERSION "4.2"

configure: exit 77


The problem seems to be happening in a header file called "confdefs.h" and the config.log file says that the program failed. I do not know what the issue is and I could greatly appreciate any help.

SPECS:
Linux kali 4.3.0-kali1-amd64

#1 SMP Debian 4.3.3-5kali4 (2016-01-13) x86_64 GNU/Linux

Gnome 3.18.2

Also, don't mind that my PATH variable references the same spot multiple times. I'll fix that shortly.

Answer

The problem seems to be happening in a header file called "confdefs.h"

confdefs.h is produced by the configure script for use in its tests. It is not your problem.

and the config.log file says that the program failed.

More specifically, it tells you exactly what command was run, and it echos the error messages that were produced and the exit status. Specifically, the command was

/usr/local/hdf-4.2.12-linux-centos7-x86_64/bin/h4cc conftest.c >&5

That's attempting to use the compiler you designated by setting the CC environment variable when you ran configure, which it earlier identified as GCC based on the output when run with the --version option.

And these errors were emitted in the failing compilation:

gcc: error: /mnt/scr1/pre-release/hdf4/v4.2.12/thg-builds/moohan-stati/lib/libmfhdf.a: No such file or directory

gcc: error: /mnt/scr1/pre-release/hdf4/v4.2.12/thg-builds/moohan-static/lib/libdf.a: No such file or directory

Those seem to be emitted every time the designated compiler is run. They are worrisome in part because diagnostics marked as errors are always worrisome, but also specifically because they suggest that the HDF4 package in which the h4cc script resides is probably incorrectly installed or incorrectly configured.

Moreover, the compiler script exited with exit status 1 (not 0) and, apparently, did not produce a compiled output file. Other outputs suggest that although it is probably a wrapper around gcc, it has its own set of options that it honors exclusively, rejecting all others, so that it is not a viable general-purpose subtitute for gcc.

I'm uncertain why you are trying to substitute the h4cc script for the system's default compiler, and the most obvious thing to try would be to not do so. If you run the configure script without defining the CC environment variable, or defining it as the path to the bare gcc binary, then the configure script should be a lot happier.

Also consult the installation instructions for the package you are trying to build. They very likely have instructions for how to point it to your HDF installation, which is likely one of the intended purposes of h4cc. Any other purposes, such as providing installation-specific compile options, should be subsumed by the build system of the package you are trying to build.