compilation error using icpc

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compilation error using icpc

Ryan P. Steele
Hi, folks -

Having a heck of a time getting openbabel installed.  I installed the
boost libraries and finally got those errors corrected.  Now I'm stuck
on one that doesn't appear obvious (to me, at least).  My C compiler
(Intel icpc) is failing the sanity check during "configure".  My
config.log is attached.  Thoughts?  I have no problem compiling other
programs with this compiler.

Thanks -
Ryan




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

It was created by Open Babel configure 2.2.3, which was
generated by GNU Autoconf 2.63.  Invocation command line was

  $ ./configure

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

hostname = ofer4-laptop
uname -m = i686
uname -r = 2.6.24-22-generic
uname -s = Linux
uname -v = #1 SMP Mon Nov 24 18:32:42 UTC 2008

/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: .
PATH: /usr
PATH: /usr/bin
PATH: /usr/lib/qt4/bin
PATH: /usr/local
PATH: /usr/local/bin
PATH: /bin
PATH: /home/ofer4
PATH: /opt/intel
PATH: /opt/intel/fc/10.1.018
PATH: /opt/intel/fc/10.1.018/bin
PATH: /opt/intel/cc/10.1.018/bin
PATH: /usr/local/texlive/2008/bin/i386-linux
PATH: /home/ofer4/mybin
PATH: /usr/local/Trolltech/Qt-4.6.2/bin
PATH: /usr/local/sbin
PATH: /usr/local/bin
PATH: /usr/sbin
PATH: /usr/bin
PATH: /sbin
PATH: /bin
PATH: /usr/games
PATH: /home/ofer4/qchem/bin/perl
PATH: /home/ofer4/qchem/bin
PATH: /home/ofer4/qchem/gbin
PATH: /home/ofer4/qchem/exe
PATH: /home/ofer4/qchem/util


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

configure:2174: checking for a BSD-compatible install
configure:2242: result: /usr/bin/install -c
configure:2253: checking whether build environment is sane
configure:2313: result: yes
configure:2454: checking for a thread-safe mkdir -p
configure:2493: result: /bin/mkdir -p
configure:2506: checking for gawk
configure:2522: found /usr/bin/gawk
configure:2533: result: gawk
configure:2544: checking whether make sets $(MAKE)
configure:2566: result: yes
configure:2640: checking whether to enable maintainer-specific portions of Makefiles
configure:2649: result: no
configure:2662: checking auto silent in maintainer mode
configure:2674: result: auto-sleep-9
configure:2729: checking build system type
configure:2747: result: i686-pc-linux-gnu
configure:2769: checking host system type
configure:2784: result: i686-pc-linux-gnu
configure:2883: checking for style of include used by make
configure:2911: result: GNU
configure:3045: checking for C++ compiler version
configure:3053: /opt/intel/cc/10.1.018/bin/icpc --version >&5
icpc (ICC) 10.1 20080801
Copyright (C) 1985-2008 Intel Corporation.  All rights reserved.

configure:3057: $? = 0
configure:3064: /opt/intel/cc/10.1.018/bin/icpc -v >&5
Version 10.1
configure:3068: $? = 0
configure:3075: /opt/intel/cc/10.1.018/bin/icpc -V >&5
Intel(R) C++ Compiler for applications running on IA-32, Version 10.1    Build 20080801 Package ID: l_cc_p_10.1.018
Copyright (C) 1985-2008 Intel Corporation.  All rights reserved.
FOR NON-COMMERCIAL USE ONLY

configure:3079: $? = 0
configure:3102: checking for C++ compiler default output file name
configure:3124: /opt/intel/cc/10.1.018/bin/icpc    conftest.cpp  >&5
configure:3128: $? = 0
configure:3166: result: a.out
configure:3185: checking whether the C++ compiler works
configure:3195: ./a.out
configure:3199: $? = 0
configure:3218: result: yes
configure:3225: checking whether we are cross compiling
configure:3227: result: no
configure:3230: checking for suffix of executables
configure:3237: /opt/intel/cc/10.1.018/bin/icpc -o conftest    conftest.cpp  >&5
configure:3241: $? = 0
configure:3267: result:
configure:3273: checking for suffix of object files
configure:3299: /opt/intel/cc/10.1.018/bin/icpc -c   conftest.cpp >&5
configure:3303: $? = 0
configure:3328: result: o
configure:3332: checking whether we are using the GNU C++ compiler
configure:3361: /opt/intel/cc/10.1.018/bin/icpc -c   conftest.cpp >&5
configure:3368: $? = 0
configure:3385: result: yes
configure:3394: checking whether /opt/intel/cc/10.1.018/bin/icpc accepts -g
configure:3424: /opt/intel/cc/10.1.018/bin/icpc -c -g  conftest.cpp >&5
configure:3431: $? = 0
configure:3532: result: yes
configure:3557: checking dependency style of /opt/intel/cc/10.1.018/bin/icpc
configure:3667: result: gcc3
configure:3713: checking for boostlib >= 1.33.1
configure:3773: /opt/intel/cc/10.1.018/bin/icpc -c -g -O2  -I/usr/include conftest.cpp >&5
configure:3780: $? = 0
configure:3786: result: yes
configure:4001: checking for gcc
configure:4028: result: /opt/intel/cc/10.1.018/bin/icc
configure:4260: checking for C compiler version
configure:4268: /opt/intel/cc/10.1.018/bin/icc --version >&5
icc (ICC) 10.1 20080801
Copyright (C) 1985-2008 Intel Corporation.  All rights reserved.

configure:4272: $? = 0
configure:4279: /opt/intel/cc/10.1.018/bin/icc -v >&5
Version 10.1
configure:4283: $? = 0
configure:4290: /opt/intel/cc/10.1.018/bin/icc -V >&5
Intel(R) C Compiler for applications running on IA-32, Version 10.1    Build 20080801 Package ID: l_cc_p_10.1.018
Copyright (C) 1985-2008 Intel Corporation.  All rights reserved.
FOR NON-COMMERCIAL USE ONLY

configure:4294: $? = 0
configure:4297: checking whether we are using the GNU C compiler
configure:4326: /opt/intel/cc/10.1.018/bin/icc -c   conftest.c >&5
configure:4333: $? = 0
configure:4350: result: yes
configure:4359: checking whether /opt/intel/cc/10.1.018/bin/icc accepts -g
configure:4389: /opt/intel/cc/10.1.018/bin/icc -c -g  conftest.c >&5
configure:4396: $? = 0
configure:4497: result: yes
configure:4514: checking for /opt/intel/cc/10.1.018/bin/icc option to accept ISO C89
configure:4588: /opt/intel/cc/10.1.018/bin/icc  -c -g -O2  conftest.c >&5
configure:4595: $? = 0
configure:4618: result: none needed
configure:4638: checking dependency style of /opt/intel/cc/10.1.018/bin/icc
configure:4748: result: gcc3
configure:4875: checking for C++ compiler version
configure:4883: /opt/intel/cc/10.1.018/bin/icpc --version >&5
icpc (ICC) 10.1 20080801
Copyright (C) 1985-2008 Intel Corporation.  All rights reserved.

configure:4887: $? = 0
configure:4894: /opt/intel/cc/10.1.018/bin/icpc -v >&5
Version 10.1
configure:4898: $? = 0
configure:4905: /opt/intel/cc/10.1.018/bin/icpc -V >&5
Intel(R) C++ Compiler for applications running on IA-32, Version 10.1    Build 20080801 Package ID: l_cc_p_10.1.018
Copyright (C) 1985-2008 Intel Corporation.  All rights reserved.
FOR NON-COMMERCIAL USE ONLY

configure:4909: $? = 0
configure:4912: checking whether we are using the GNU C++ compiler
configure:4965: result: yes
configure:4974: checking whether /opt/intel/cc/10.1.018/bin/icpc accepts -g
configure:5112: result: yes
configure:5137: checking dependency style of /opt/intel/cc/10.1.018/bin/icpc
configure:5247: result: gcc3
configure:5267: checking how to run the C++ preprocessor
configure:5303: /opt/intel/cc/10.1.018/bin/icpc -E  conftest.cpp
configure:5310: $? = 0
configure:5341: /opt/intel/cc/10.1.018/bin/icpc -E  conftest.cpp
conftest.cpp(11): error #5: could not open source file "ac_nonexistent.h"
  #include <ac_nonexistent.h>
                             ^

configure:5348: $? = 2
configure: failed program was:
| /* confdefs.h.  */
| #define PACKAGE_NAME "Open Babel"
| #define PACKAGE_TARNAME "openbabel"
| #define PACKAGE_VERSION "2.2.3"
| #define PACKAGE_STRING "Open Babel 2.2.3"
| #define PACKAGE_BUGREPORT "[hidden email]"
| #define BABEL_VERSION "2.2.3"
| #define BABEL_DATADIR "/usr/local/share/openbabel"
| #define HAVE_BOOST /**/
| /* end confdefs.h.  */
| #include <ac_nonexistent.h>
configure:5381: result: /opt/intel/cc/10.1.018/bin/icpc -E
configure:5410: /opt/intel/cc/10.1.018/bin/icpc -E  conftest.cpp
configure:5417: $? = 0
configure:5448: /opt/intel/cc/10.1.018/bin/icpc -E  conftest.cpp
conftest.cpp(11): error #5: could not open source file "ac_nonexistent.h"
  #include <ac_nonexistent.h>
                             ^

configure:5455: $? = 2
configure: failed program was:
| /* confdefs.h.  */
| #define PACKAGE_NAME "Open Babel"
| #define PACKAGE_TARNAME "openbabel"
| #define PACKAGE_VERSION "2.2.3"
| #define PACKAGE_STRING "Open Babel 2.2.3"
| #define PACKAGE_BUGREPORT "[hidden email]"
| #define BABEL_VERSION "2.2.3"
| #define BABEL_DATADIR "/usr/local/share/openbabel"
| #define HAVE_BOOST /**/
| /* end confdefs.h.  */
| #include <ac_nonexistent.h>
configure:5508: checking for a BSD-compatible install
configure:5576: result: /usr/bin/install -c
configure:5589: checking for doxygen
configure:5607: found /usr/bin/doxygen
configure:5619: result: /usr/bin/doxygen
configure:5629: checking for swig
configure:5662: result: no
configure:5669: checking for perl
configure:5687: found /usr/bin/perl
configure:5699: result: /usr/bin/perl
configure:5709: checking for prove
configure:5727: found /usr/bin/prove
configure:5739: result: /usr/bin/prove
configure:5749: checking for python
configure:5767: found /usr/bin/python
configure:5779: result: /usr/bin/python
configure:5789: checking for ruby
configure:5807: found /usr/bin/ruby
configure:5819: result: /usr/bin/ruby
configure:5831: checking for gmcs
configure:5864: result: no
configure:5875: checking for javac
configure:5908: result: no
configure:5915: checking for jar
configure:5948: result: no
configure:5958: checking for wx-config
configure:5976: found /usr/local/bin/wx-config
configure:5988: result: /usr/local/bin/wx-config
configure:6443: checking for a sed that does not truncate output
configure:6509: result: /bin/sed
configure:6527: checking for grep that handles long lines and -e
configure:6587: result: /bin/grep
configure:6592: checking for egrep
configure:6656: result: /bin/grep -E
configure:6661: checking for fgrep
configure:6725: result: /bin/grep -F
configure:6760: checking for ld used by /opt/intel/cc/10.1.018/bin/icc
configure:6827: result: /usr/bin/ld
configure:6836: checking if the linker (/usr/bin/ld) is GNU ld
configure:6851: result: yes
configure:6863: checking for BSD- or MS-compatible name lister (nm)
configure:6912: result: /usr/bin/nm -B
configure:7030: checking the name lister (/usr/bin/nm -B) interface
configure:7037: /opt/intel/cc/10.1.018/bin/icc -c -g -O2  conftest.c >&5
configure:7040: /usr/bin/nm -B "conftest.o"
configure:7043: output
00000000 N .debug_info_seg
00000000 B some_variable
configure:7050: result: BSD nm
configure:7053: checking whether ln -s works
configure:7057: result: yes
configure:7065: checking the maximum length of command line arguments
configure:7185: result: 98304
configure:7202: checking whether the shell understands some XSI constructs
configure:7212: result: yes
configure:7216: checking whether the shell understands "+="
configure:7222: result: yes
configure:7257: checking for /usr/bin/ld option to reload object files
configure:7264: result: -r
configure:7333: checking for objdump
configure:7360: result: objdump
configure:7389: checking how to recognize dependent libraries
configure:7585: result: pass_all
configure:7645: checking for ar
configure:7661: found /usr/bin/ar
configure:7672: result: ar
configure:7750: checking for strip
configure:7766: found /usr/bin/strip
configure:7777: result: strip
configure:7849: checking for ranlib
configure:7865: found /usr/bin/ranlib
configure:7876: result: ranlib
configure:7966: checking command to parse /usr/bin/nm -B output from /opt/intel/cc/10.1.018/bin/icc object
configure:8084: /opt/intel/cc/10.1.018/bin/icc -c -g -O2  conftest.c >&5
configure:8087: $? = 0
configure:8091: /usr/bin/nm -B conftest.o \| sed -n -e 's/^.*[ ]\([ABCDGIRSTW][ABCDGIRSTW]*\)[ ][ ]*\([_A-Za-z][_A-Za-z0-9]*\)$/\1 \2 \2/p' \> conftest.nm
configure:8094: $? = 0
configure:8148: /opt/intel/cc/10.1.018/bin/icc -o conftest -g -O2   conftest.c conftstm.o >&5
configure:8151: $? = 0
configure:8189: result: ok
configure:9056: checking how to run the C preprocessor
configure:9174: result: /opt/intel/cc/10.1.018/bin/icpc
configure:9203: /opt/intel/cc/10.1.018/bin/icpc  conftest.c
conftest.c(16): error: identifier "Syntax" is undefined
      Syntax error
      ^

conftest.c(16): error: expected a ";"

compilation aborted for conftest.c (code 2)
configure:9210: $? = 2
configure: failed program was:
| /* confdefs.h.  */
| #define PACKAGE_NAME "Open Babel"
| #define PACKAGE_TARNAME "openbabel"
| #define PACKAGE_VERSION "2.2.3"
| #define PACKAGE_STRING "Open Babel 2.2.3"
| #define PACKAGE_BUGREPORT "[hidden email]"
| #define BABEL_VERSION "2.2.3"
| #define BABEL_DATADIR "/usr/local/share/openbabel"
| #define HAVE_BOOST /**/
| /* end confdefs.h.  */
| #ifdef __STDC__
| # include <limits.h>
| #else
| # include <assert.h>
| #endif
|     Syntax error
configure:9203: /opt/intel/cc/10.1.018/bin/icpc  conftest.c
conftest.c(16): error: identifier "Syntax" is undefined
      Syntax error
      ^

conftest.c(16): error: expected a ";"

compilation aborted for conftest.c (code 2)
configure:9210: $? = 2
configure: failed program was:
| /* confdefs.h.  */
| #define PACKAGE_NAME "Open Babel"
| #define PACKAGE_TARNAME "openbabel"
| #define PACKAGE_VERSION "2.2.3"
| #define PACKAGE_STRING "Open Babel 2.2.3"
| #define PACKAGE_BUGREPORT "[hidden email]"
| #define BABEL_VERSION "2.2.3"
| #define BABEL_DATADIR "/usr/local/share/openbabel"
| #define HAVE_BOOST /**/
| /* end confdefs.h.  */
| #ifdef __STDC__
| # include <limits.h>
| #else
| # include <assert.h>
| #endif
|     Syntax error
configure:9272: error: in `/home/ofer4/Downloads/openbabel-2.2.3':
configure:9275: error: C preprocessor "/opt/intel/cc/10.1.018/bin/icpc" fails sanity check
See `config.log' for more details.

## ---------------- ##
## Cache variables. ##
## ---------------- ##

ac_cv_build=i686-pc-linux-gnu
ac_cv_c_compiler_gnu=yes
ac_cv_cxx_compiler_gnu=yes
ac_cv_env_CCC_set=
ac_cv_env_CCC_value=
ac_cv_env_CC_set=set
ac_cv_env_CC_value=/opt/intel/cc/10.1.018/bin/icc
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=set
ac_cv_env_CPP_value=/opt/intel/cc/10.1.018/bin/icpc
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=set
ac_cv_env_CXX_value=/opt/intel/cc/10.1.018/bin/icpc
ac_cv_env_LDFLAGS_set=
ac_cv_env_LDFLAGS_value=
ac_cv_env_LIBS_set=
ac_cv_env_LIBS_value=
ac_cv_env_WXCONFIG_set=
ac_cv_env_WXCONFIG_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=i686-pc-linux-gnu
ac_cv_objext=o
ac_cv_path_DOXYGEN=/usr/bin/doxygen
ac_cv_path_EGREP='/bin/grep -E'
ac_cv_path_FGREP='/bin/grep -F'
ac_cv_path_GREP=/bin/grep
ac_cv_path_PERL=/usr/bin/perl
ac_cv_path_PROVE=/usr/bin/prove
ac_cv_path_PYTHON=/usr/bin/python
ac_cv_path_RUBY=/usr/bin/ruby
ac_cv_path_SED=/bin/sed
ac_cv_path_WXCONFIG=/usr/local/bin/wx-config
ac_cv_path_install='/usr/bin/install -c'
ac_cv_path_mkdir=/bin/mkdir
ac_cv_prog_AWK=gawk
ac_cv_prog_CPP=/opt/intel/cc/10.1.018/bin/icpc
ac_cv_prog_CXXCPP='/opt/intel/cc/10.1.018/bin/icpc -E'
ac_cv_prog_ac_ct_AR=ar
ac_cv_prog_ac_ct_CC=/opt/intel/cc/10.1.018/bin/icc
ac_cv_prog_ac_ct_OBJDUMP=objdump
ac_cv_prog_ac_ct_RANLIB=ranlib
ac_cv_prog_ac_ct_STRIP=strip
ac_cv_prog_cc_c89=
ac_cv_prog_cc_g=yes
ac_cv_prog_cxx_g=yes
ac_cv_prog_make_make_set=yes
am_cv_CC_dependencies_compiler_type=gcc3
am_cv_CXX_dependencies_compiler_type=gcc3
lt_cv_deplibs_check_method=pass_all
lt_cv_file_magic_cmd='$MAGIC_CMD'
lt_cv_file_magic_test_file=
lt_cv_ld_reload_flag=-r
lt_cv_nm_interface='BSD nm'
lt_cv_path_LD=/usr/bin/ld
lt_cv_path_NM='/usr/bin/nm -B'
lt_cv_prog_gnu_ld=yes
lt_cv_sys_global_symbol_pipe='sed -n -e '\''s/^.*[ ]\([ABCDGIRSTW][ABCDGIRSTW]*\)[ ][ ]*\([_A-Za-z][_A-Za-z0-9]*\)$/\1 \2 \2/p'\'''
lt_cv_sys_global_symbol_to_c_name_address='sed -n -e '\''s/^: \([^ ]*\) $/  {\"\1\", (void *) 0},/p'\'' -e '\''s/^[ABCDGIRSTW]* \([^ ]*\) \([^ ]*\)$/  {"\2", (void *) \&\2},/p'\'''
lt_cv_sys_global_symbol_to_c_name_address_lib_prefix='sed -n -e '\''s/^: \([^ ]*\) $/  {\"\1\", (void *) 0},/p'\'' -e '\''s/^[ABCDGIRSTW]* \([^ ]*\) \(lib[^ ]*\)$/  {"\2", (void *) \&\2},/p'\'' -e '\''s/^[ABCDGIRSTW]* \([^ ]*\) \([^ ]*\)$/  {"lib\2", (void *) \&\2},/p'\'''
lt_cv_sys_global_symbol_to_cdecl='sed -n -e '\''s/^T .* \(.*\)$/extern int \1();/p'\'' -e '\''s/^[ABCDGIRSTW]* .* \(.*\)$/extern char \1;/p'\'''
lt_cv_sys_max_cmd_len=98304

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

ACLOCAL='${SHELL} /home/ofer4/Downloads/openbabel-2.2.3/missing --run aclocal-1.11'
AMDEPBACKSLASH='\'
AMDEP_FALSE='#'
AMDEP_TRUE=''
AMTAR='${SHELL} /home/ofer4/Downloads/openbabel-2.2.3/missing --run tar'
AR='ar'
AS='as'
AUTOCONF='sleep 9 ; true || autoconf || skipped'
AUTOHEADER='sleep 9 ; true || autoheader || skipped'
AUTOMAKE='sleep 9 ; true || automake || skipped'
AWK='gawk'
BIN2HEX_FALSE='#'
BIN2HEX_TRUE=''
BOOST_CPPFLAGS='-I/usr/include'
BOOST_LDFLAGS='-L/usr/lib'
BUILD_CSHARP_FALSE='#'
BUILD_CSHARP_TRUE=''
BUILD_DOCS_FALSE='#'
BUILD_DOCS_TRUE=''
BUILD_INCHI_FALSE=''
BUILD_INCHI_TRUE=''
BUILD_JAVA_FALSE=''
BUILD_JAVA_TRUE='#'
BUILD_PCH_FALSE=''
BUILD_PCH_TRUE=''
BUILD_RUBY_FALSE='#'
BUILD_RUBY_TRUE=''
BUILD_SCRIPTS_FALSE='#'
BUILD_SCRIPTS_TRUE=''
BUILD_SHARED_FALSE=''
BUILD_SHARED_TRUE=''
BUILD_SHARED_UNIX_FALSE=''
BUILD_SHARED_UNIX_TRUE=''
BUILD_SHARED_WIN_FALSE=''
BUILD_SHARED_WIN_TRUE=''
BUILD_SWIG_FALSE=''
BUILD_SWIG_TRUE='#'
BUILD_WXGUI_FALSE=''
BUILD_WXGUI_TRUE='#'
BUILD_XML_FALSE=''
BUILD_XML_TRUE=''
BUILD_ZLIB_FALSE=''
BUILD_ZLIB_TRUE=''
CC='/opt/intel/cc/10.1.018/bin/icc'
CCDEPMODE='depmode=gcc3'
CFLAGS='-g -O2'
CPP='/opt/intel/cc/10.1.018/bin/icpc'
CPPFLAGS=''
CSHARP='mcs'
CXX='/opt/intel/cc/10.1.018/bin/icpc'
CXXCPP='/opt/intel/cc/10.1.018/bin/icpc -E'
CXXDEPMODE='depmode=gcc3'
CXXFLAGS='-g -O2'
CYGPATH_W='echo'
DEFS=''
DEPDIR='.deps'
DLLTOOL='dlltool'
DOXYGEN='/usr/bin/doxygen'
DSYMUTIL=''
DUMPBIN=''
ECHO_C=''
ECHO_N='-n'
ECHO_T=''
EGREP='/bin/grep -E'
EXEEXT=''
FGREP='/bin/grep -F'
GREP='/bin/grep'
HAVE_REGEX_FALSE=''
HAVE_REGEX_TRUE=''
HAVE_SHARED_POINTER_FALSE=''
HAVE_SHARED_POINTER_TRUE=''
INSTALL_DATA='${INSTALL} -m 644'
INSTALL_PROGRAM='${INSTALL}'
INSTALL_SCRIPT='${INSTALL}'
INSTALL_STRIP_PROGRAM='$(install_sh) -c -s'
JAR=''
JAVAC=''
LD='/usr/bin/ld'
LDFLAGS=''
LIBDL=''
LIBOBJS=''
LIBS=''
LIBTOOL=''
LIPO=''
LN_S='ln -s'
LTLIBOBJS=''
MAINT='#'
MAINTAINER_MODE_FALSE=''
MAINTAINER_MODE_TRUE='#'
MAKEINFO='${SHELL} /home/ofer4/Downloads/openbabel-2.2.3/missing --run makeinfo'
MKDIR_P='/bin/mkdir -p'
NM='/usr/bin/nm -B'
NMEDIT=''
OBJDUMP='objdump'
OBJEXT='o'
OTOOL64=''
OTOOL=''
PACKAGE='openbabel'
PACKAGE_BUGREPORT='[hidden email]'
PACKAGE_NAME='Open Babel'
PACKAGE_STRING='Open Babel 2.2.3'
PACKAGE_TARNAME='openbabel'
PACKAGE_VERSION='2.2.3'
PATH_SEPARATOR=':'
PERL='/usr/bin/perl'
PERL_TESTS_FALSE='#'
PERL_TESTS_TRUE=''
PROVE='/usr/bin/prove'
PYTHON='/usr/bin/python'
RANLIB='ranlib'
RUBY='/usr/bin/ruby'
SED='/bin/sed'
SET_MAKE=''
SHELL='/bin/bash'
STRIP='strip'
SWIG=''
USE_BOOST_FLAGS_FALSE=''
USE_BOOST_FLAGS_TRUE=''
VERSION='2.2.3'
WXCONFIG='/usr/local/bin/wx-config'
WX_CPPFLAGS=''
WX_CXXFLAGS=''
WX_LIBS=''
XML2_CONFIG=''
XML_CPPFLAGS=''
XML_LIBS=''
ac_ct_CC='/opt/intel/cc/10.1.018/bin/icc'
ac_ct_CXX=''
ac_ct_DUMPBIN=''
am__EXEEXT_FALSE=''
am__EXEEXT_TRUE=''
am__fastdepCC_FALSE='#'
am__fastdepCC_TRUE=''
am__fastdepCXX_FALSE='#'
am__fastdepCXX_TRUE=''
am__include='include'
am__isrc=''
am__leading_dot='.'
am__quote=''
am__tar='${AMTAR} chof - "$$tardir"'
am__untar='${AMTAR} xf -'
bindir='${exec_prefix}/bin'
build='i686-pc-linux-gnu'
build_alias=''
build_cpu='i686'
build_os='linux-gnu'
build_vendor='pc'
datadir='${datarootdir}'
datarootdir='${prefix}/share'
docdir='${datarootdir}/doc/${PACKAGE_TARNAME}'
dvidir='${docdir}'
exec_prefix='${prefix}'
host='i686-pc-linux-gnu'
host_alias=''
host_cpu='i686'
host_os='linux-gnu'
host_vendor='pc'
htmldir='${docdir}'
includedir='${prefix}/include'
infodir='${datarootdir}/info'
install_sh='${SHELL} /home/ofer4/Downloads/openbabel-2.2.3/install-sh'
libdir='${exec_prefix}/lib'
libexecdir='${exec_prefix}/libexec'
localedir='${datarootdir}/locale'
localstatedir='${prefix}/var'
lt_ECHO='echo'
mandir='${datarootdir}/man'
mkdir_p='/bin/mkdir -p'
oldincludedir='/usr/include'
pdfdir='${docdir}'
pkglibdir=''
prefix='/usr/local'
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 "Open Babel"
#define PACKAGE_TARNAME "openbabel"
#define PACKAGE_VERSION "2.2.3"
#define PACKAGE_STRING "Open Babel 2.2.3"
#define PACKAGE_BUGREPORT "[hidden email]"
#define BABEL_VERSION "2.2.3"
#define BABEL_DATADIR "/usr/local/share/openbabel"
#define HAVE_BOOST /**/

configure: exit 1

------------------------------------------------------------------------------

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Re: compilation error using icpc

Noel O'Boyle
Administrator
Hi Ryan,

I see you're using Intel Compiler 10.1.018. I have compiled OB with
Intel Compiler 11.1.059 without problem (and without BOOST). Do you
have access to a newer compiler, or even to gcc?

- Noel

On 28 April 2010 23:34, Ryan P. Steele <[hidden email]> wrote:

> Hi, folks -
>
> Having a heck of a time getting openbabel installed.  I installed the boost
> libraries and finally got those errors corrected.  Now I'm stuck on one that
> doesn't appear obvious (to me, at least).  My C compiler (Intel icpc) is
> failing the sanity check during "configure".  My config.log is attached.
>  Thoughts?  I have no problem compiling other programs with this compiler.
>
> Thanks -
> Ryan
>
>
>
>
> This file contains any messages produced by compilers while
> running configure, to aid debugging if configure makes a mistake.
>
> It was created by Open Babel configure 2.2.3, which was
> generated by GNU Autoconf 2.63.  Invocation command line was
>
>  $ ./configure
>
> ## --------- ##
> ## Platform. ##
> ## --------- ##
>
> hostname = ofer4-laptop
> uname -m = i686
> uname -r = 2.6.24-22-generic
> uname -s = Linux
> uname -v = #1 SMP Mon Nov 24 18:32:42 UTC 2008
>
> /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: .
> PATH: /usr
> PATH: /usr/bin
> PATH: /usr/lib/qt4/bin
> PATH: /usr/local
> PATH: /usr/local/bin
> PATH: /bin
> PATH: /home/ofer4
> PATH: /opt/intel
> PATH: /opt/intel/fc/10.1.018
> PATH: /opt/intel/fc/10.1.018/bin
> PATH: /opt/intel/cc/10.1.018/bin
> PATH: /usr/local/texlive/2008/bin/i386-linux
> PATH: /home/ofer4/mybin
> PATH: /usr/local/Trolltech/Qt-4.6.2/bin
> PATH: /usr/local/sbin
> PATH: /usr/local/bin
> PATH: /usr/sbin
> PATH: /usr/bin
> PATH: /sbin
> PATH: /bin
> PATH: /usr/games
> PATH: /home/ofer4/qchem/bin/perl
> PATH: /home/ofer4/qchem/bin
> PATH: /home/ofer4/qchem/gbin
> PATH: /home/ofer4/qchem/exe
> PATH: /home/ofer4/qchem/util
>
>
> ## ----------- ##
> ## Core tests. ##
> ## ----------- ##
>
> configure:2174: checking for a BSD-compatible install
> configure:2242: result: /usr/bin/install -c
> configure:2253: checking whether build environment is sane
> configure:2313: result: yes
> configure:2454: checking for a thread-safe mkdir -p
> configure:2493: result: /bin/mkdir -p
> configure:2506: checking for gawk
> configure:2522: found /usr/bin/gawk
> configure:2533: result: gawk
> configure:2544: checking whether make sets $(MAKE)
> configure:2566: result: yes
> configure:2640: checking whether to enable maintainer-specific portions of
> Makefiles
> configure:2649: result: no
> configure:2662: checking auto silent in maintainer mode
> configure:2674: result: auto-sleep-9
> configure:2729: checking build system type
> configure:2747: result: i686-pc-linux-gnu
> configure:2769: checking host system type
> configure:2784: result: i686-pc-linux-gnu
> configure:2883: checking for style of include used by make
> configure:2911: result: GNU
> configure:3045: checking for C++ compiler version
> configure:3053: /opt/intel/cc/10.1.018/bin/icpc --version >&5
> icpc (ICC) 10.1 20080801
> Copyright (C) 1985-2008 Intel Corporation.  All rights reserved.
>
> configure:3057: $? = 0
> configure:3064: /opt/intel/cc/10.1.018/bin/icpc -v >&5
> Version 10.1
> configure:3068: $? = 0
> configure:3075: /opt/intel/cc/10.1.018/bin/icpc -V >&5
> Intel(R) C++ Compiler for applications running on IA-32, Version 10.1
>  Build 20080801 Package ID: l_cc_p_10.1.018
> Copyright (C) 1985-2008 Intel Corporation.  All rights reserved.
> FOR NON-COMMERCIAL USE ONLY
>
> configure:3079: $? = 0
> configure:3102: checking for C++ compiler default output file name
> configure:3124: /opt/intel/cc/10.1.018/bin/icpc    conftest.cpp  >&5
> configure:3128: $? = 0
> configure:3166: result: a.out
> configure:3185: checking whether the C++ compiler works
> configure:3195: ./a.out
> configure:3199: $? = 0
> configure:3218: result: yes
> configure:3225: checking whether we are cross compiling
> configure:3227: result: no
> configure:3230: checking for suffix of executables
> configure:3237: /opt/intel/cc/10.1.018/bin/icpc -o conftest    conftest.cpp
>  >&5
> configure:3241: $? = 0
> configure:3267: result:
> configure:3273: checking for suffix of object files
> configure:3299: /opt/intel/cc/10.1.018/bin/icpc -c   conftest.cpp >&5
> configure:3303: $? = 0
> configure:3328: result: o
> configure:3332: checking whether we are using the GNU C++ compiler
> configure:3361: /opt/intel/cc/10.1.018/bin/icpc -c   conftest.cpp >&5
> configure:3368: $? = 0
> configure:3385: result: yes
> configure:3394: checking whether /opt/intel/cc/10.1.018/bin/icpc accepts -g
> configure:3424: /opt/intel/cc/10.1.018/bin/icpc -c -g  conftest.cpp >&5
> configure:3431: $? = 0
> configure:3532: result: yes
> configure:3557: checking dependency style of /opt/intel/cc/10.1.018/bin/icpc
> configure:3667: result: gcc3
> configure:3713: checking for boostlib >= 1.33.1
> configure:3773: /opt/intel/cc/10.1.018/bin/icpc -c -g -O2  -I/usr/include
> conftest.cpp >&5
> configure:3780: $? = 0
> configure:3786: result: yes
> configure:4001: checking for gcc
> configure:4028: result: /opt/intel/cc/10.1.018/bin/icc
> configure:4260: checking for C compiler version
> configure:4268: /opt/intel/cc/10.1.018/bin/icc --version >&5
> icc (ICC) 10.1 20080801
> Copyright (C) 1985-2008 Intel Corporation.  All rights reserved.
>
> configure:4272: $? = 0
> configure:4279: /opt/intel/cc/10.1.018/bin/icc -v >&5
> Version 10.1
> configure:4283: $? = 0
> configure:4290: /opt/intel/cc/10.1.018/bin/icc -V >&5
> Intel(R) C Compiler for applications running on IA-32, Version 10.1    Build
> 20080801 Package ID: l_cc_p_10.1.018
> Copyright (C) 1985-2008 Intel Corporation.  All rights reserved.
> FOR NON-COMMERCIAL USE ONLY
>
> configure:4294: $? = 0
> configure:4297: checking whether we are using the GNU C compiler
> configure:4326: /opt/intel/cc/10.1.018/bin/icc -c   conftest.c >&5
> configure:4333: $? = 0
> configure:4350: result: yes
> configure:4359: checking whether /opt/intel/cc/10.1.018/bin/icc accepts -g
> configure:4389: /opt/intel/cc/10.1.018/bin/icc -c -g  conftest.c >&5
> configure:4396: $? = 0
> configure:4497: result: yes
> configure:4514: checking for /opt/intel/cc/10.1.018/bin/icc option to accept
> ISO C89
> configure:4588: /opt/intel/cc/10.1.018/bin/icc  -c -g -O2  conftest.c >&5
> configure:4595: $? = 0
> configure:4618: result: none needed
> configure:4638: checking dependency style of /opt/intel/cc/10.1.018/bin/icc
> configure:4748: result: gcc3
> configure:4875: checking for C++ compiler version
> configure:4883: /opt/intel/cc/10.1.018/bin/icpc --version >&5
> icpc (ICC) 10.1 20080801
> Copyright (C) 1985-2008 Intel Corporation.  All rights reserved.
>
> configure:4887: $? = 0
> configure:4894: /opt/intel/cc/10.1.018/bin/icpc -v >&5
> Version 10.1
> configure:4898: $? = 0
> configure:4905: /opt/intel/cc/10.1.018/bin/icpc -V >&5
> Intel(R) C++ Compiler for applications running on IA-32, Version 10.1
>  Build 20080801 Package ID: l_cc_p_10.1.018
> Copyright (C) 1985-2008 Intel Corporation.  All rights reserved.
> FOR NON-COMMERCIAL USE ONLY
>
> configure:4909: $? = 0
> configure:4912: checking whether we are using the GNU C++ compiler
> configure:4965: result: yes
> configure:4974: checking whether /opt/intel/cc/10.1.018/bin/icpc accepts -g
> configure:5112: result: yes
> configure:5137: checking dependency style of /opt/intel/cc/10.1.018/bin/icpc
> configure:5247: result: gcc3
> configure:5267: checking how to run the C++ preprocessor
> configure:5303: /opt/intel/cc/10.1.018/bin/icpc -E  conftest.cpp
> configure:5310: $? = 0
> configure:5341: /opt/intel/cc/10.1.018/bin/icpc -E  conftest.cpp
> conftest.cpp(11): error #5: could not open source file "ac_nonexistent.h"
>  #include <ac_nonexistent.h>
>                             ^
>
> configure:5348: $? = 2
> configure: failed program was:
> | /* confdefs.h.  */
> | #define PACKAGE_NAME "Open Babel"
> | #define PACKAGE_TARNAME "openbabel"
> | #define PACKAGE_VERSION "2.2.3"
> | #define PACKAGE_STRING "Open Babel 2.2.3"
> | #define PACKAGE_BUGREPORT "[hidden email]"
> | #define BABEL_VERSION "2.2.3"
> | #define BABEL_DATADIR "/usr/local/share/openbabel"
> | #define HAVE_BOOST /**/
> | /* end confdefs.h.  */
> | #include <ac_nonexistent.h>
> configure:5381: result: /opt/intel/cc/10.1.018/bin/icpc -E
> configure:5410: /opt/intel/cc/10.1.018/bin/icpc -E  conftest.cpp
> configure:5417: $? = 0
> configure:5448: /opt/intel/cc/10.1.018/bin/icpc -E  conftest.cpp
> conftest.cpp(11): error #5: could not open source file "ac_nonexistent.h"
>  #include <ac_nonexistent.h>
>                             ^
>
> configure:5455: $? = 2
> configure: failed program was:
> | /* confdefs.h.  */
> | #define PACKAGE_NAME "Open Babel"
> | #define PACKAGE_TARNAME "openbabel"
> | #define PACKAGE_VERSION "2.2.3"
> | #define PACKAGE_STRING "Open Babel 2.2.3"
> | #define PACKAGE_BUGREPORT "[hidden email]"
> | #define BABEL_VERSION "2.2.3"
> | #define BABEL_DATADIR "/usr/local/share/openbabel"
> | #define HAVE_BOOST /**/
> | /* end confdefs.h.  */
> | #include <ac_nonexistent.h>
> configure:5508: checking for a BSD-compatible install
> configure:5576: result: /usr/bin/install -c
> configure:5589: checking for doxygen
> configure:5607: found /usr/bin/doxygen
> configure:5619: result: /usr/bin/doxygen
> configure:5629: checking for swig
> configure:5662: result: no
> configure:5669: checking for perl
> configure:5687: found /usr/bin/perl
> configure:5699: result: /usr/bin/perl
> configure:5709: checking for prove
> configure:5727: found /usr/bin/prove
> configure:5739: result: /usr/bin/prove
> configure:5749: checking for python
> configure:5767: found /usr/bin/python
> configure:5779: result: /usr/bin/python
> configure:5789: checking for ruby
> configure:5807: found /usr/bin/ruby
> configure:5819: result: /usr/bin/ruby
> configure:5831: checking for gmcs
> configure:5864: result: no
> configure:5875: checking for javac
> configure:5908: result: no
> configure:5915: checking for jar
> configure:5948: result: no
> configure:5958: checking for wx-config
> configure:5976: found /usr/local/bin/wx-config
> configure:5988: result: /usr/local/bin/wx-config
> configure:6443: checking for a sed that does not truncate output
> configure:6509: result: /bin/sed
> configure:6527: checking for grep that handles long lines and -e
> configure:6587: result: /bin/grep
> configure:6592: checking for egrep
> configure:6656: result: /bin/grep -E
> configure:6661: checking for fgrep
> configure:6725: result: /bin/grep -F
> configure:6760: checking for ld used by /opt/intel/cc/10.1.018/bin/icc
> configure:6827: result: /usr/bin/ld
> configure:6836: checking if the linker (/usr/bin/ld) is GNU ld
> configure:6851: result: yes
> configure:6863: checking for BSD- or MS-compatible name lister (nm)
> configure:6912: result: /usr/bin/nm -B
> configure:7030: checking the name lister (/usr/bin/nm -B) interface
> configure:7037: /opt/intel/cc/10.1.018/bin/icc -c -g -O2  conftest.c >&5
> configure:7040: /usr/bin/nm -B "conftest.o"
> configure:7043: output
> 00000000 N .debug_info_seg
> 00000000 B some_variable
> configure:7050: result: BSD nm
> configure:7053: checking whether ln -s works
> configure:7057: result: yes
> configure:7065: checking the maximum length of command line arguments
> configure:7185: result: 98304
> configure:7202: checking whether the shell understands some XSI constructs
> configure:7212: result: yes
> configure:7216: checking whether the shell understands "+="
> configure:7222: result: yes
> configure:7257: checking for /usr/bin/ld option to reload object files
> configure:7264: result: -r
> configure:7333: checking for objdump
> configure:7360: result: objdump
> configure:7389: checking how to recognize dependent libraries
> configure:7585: result: pass_all
> configure:7645: checking for ar
> configure:7661: found /usr/bin/ar
> configure:7672: result: ar
> configure:7750: checking for strip
> configure:7766: found /usr/bin/strip
> configure:7777: result: strip
> configure:7849: checking for ranlib
> configure:7865: found /usr/bin/ranlib
> configure:7876: result: ranlib
> configure:7966: checking command to parse /usr/bin/nm -B output from
> /opt/intel/cc/10.1.018/bin/icc object
> configure:8084: /opt/intel/cc/10.1.018/bin/icc -c -g -O2  conftest.c >&5
> configure:8087: $? = 0
> configure:8091: /usr/bin/nm -B conftest.o \| sed -n -e 's/^.*[
> ]\([ABCDGIRSTW][ABCDGIRSTW]*\)[         ][
>  ]*\([_A-Za-z][_A-Za-z0-9]*\)$/\1 \2 \2/p' \> conftest.nm
> configure:8094: $? = 0
> configure:8148: /opt/intel/cc/10.1.018/bin/icc -o conftest -g -O2
> conftest.c conftstm.o >&5
> configure:8151: $? = 0
> configure:8189: result: ok
> configure:9056: checking how to run the C preprocessor
> configure:9174: result: /opt/intel/cc/10.1.018/bin/icpc
> configure:9203: /opt/intel/cc/10.1.018/bin/icpc  conftest.c
> conftest.c(16): error: identifier "Syntax" is undefined
>                     Syntax error
>                     ^
>
> conftest.c(16): error: expected a ";"
>
> compilation aborted for conftest.c (code 2)
> configure:9210: $? = 2
> configure: failed program was:
> | /* confdefs.h.  */
> | #define PACKAGE_NAME "Open Babel"
> | #define PACKAGE_TARNAME "openbabel"
> | #define PACKAGE_VERSION "2.2.3"
> | #define PACKAGE_STRING "Open Babel 2.2.3"
> | #define PACKAGE_BUGREPORT "[hidden email]"
> | #define BABEL_VERSION "2.2.3"
> | #define BABEL_DATADIR "/usr/local/share/openbabel"
> | #define HAVE_BOOST /**/
> | /* end confdefs.h.  */
> | #ifdef __STDC__
> | # include <limits.h>
> | #else
> | # include <assert.h>
> | #endif
> |                    Syntax error
> configure:9203: /opt/intel/cc/10.1.018/bin/icpc  conftest.c
> conftest.c(16): error: identifier "Syntax" is undefined
>                     Syntax error
>                     ^
>
> conftest.c(16): error: expected a ";"
>
> compilation aborted for conftest.c (code 2)
> configure:9210: $? = 2
> configure: failed program was:
> | /* confdefs.h.  */
> | #define PACKAGE_NAME "Open Babel"
> | #define PACKAGE_TARNAME "openbabel"
> | #define PACKAGE_VERSION "2.2.3"
> | #define PACKAGE_STRING "Open Babel 2.2.3"
> | #define PACKAGE_BUGREPORT "[hidden email]"
> | #define BABEL_VERSION "2.2.3"
> | #define BABEL_DATADIR "/usr/local/share/openbabel"
> | #define HAVE_BOOST /**/
> | /* end confdefs.h.  */
> | #ifdef __STDC__
> | # include <limits.h>
> | #else
> | # include <assert.h>
> | #endif
> |                    Syntax error
> configure:9272: error: in `/home/ofer4/Downloads/openbabel-2.2.3':
> configure:9275: error: C preprocessor "/opt/intel/cc/10.1.018/bin/icpc"
> fails sanity check
> See `config.log' for more details.
>
> ## ---------------- ##
> ## Cache variables. ##
> ## ---------------- ##
>
> ac_cv_build=i686-pc-linux-gnu
> ac_cv_c_compiler_gnu=yes
> ac_cv_cxx_compiler_gnu=yes
> ac_cv_env_CCC_set=
> ac_cv_env_CCC_value=
> ac_cv_env_CC_set=set
> ac_cv_env_CC_value=/opt/intel/cc/10.1.018/bin/icc
> 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=set
> ac_cv_env_CPP_value=/opt/intel/cc/10.1.018/bin/icpc
> 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=set
> ac_cv_env_CXX_value=/opt/intel/cc/10.1.018/bin/icpc
> ac_cv_env_LDFLAGS_set=
> ac_cv_env_LDFLAGS_value=
> ac_cv_env_LIBS_set=
> ac_cv_env_LIBS_value=
> ac_cv_env_WXCONFIG_set=
> ac_cv_env_WXCONFIG_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=i686-pc-linux-gnu
> ac_cv_objext=o
> ac_cv_path_DOXYGEN=/usr/bin/doxygen
> ac_cv_path_EGREP='/bin/grep -E'
> ac_cv_path_FGREP='/bin/grep -F'
> ac_cv_path_GREP=/bin/grep
> ac_cv_path_PERL=/usr/bin/perl
> ac_cv_path_PROVE=/usr/bin/prove
> ac_cv_path_PYTHON=/usr/bin/python
> ac_cv_path_RUBY=/usr/bin/ruby
> ac_cv_path_SED=/bin/sed
> ac_cv_path_WXCONFIG=/usr/local/bin/wx-config
> ac_cv_path_install='/usr/bin/install -c'
> ac_cv_path_mkdir=/bin/mkdir
> ac_cv_prog_AWK=gawk
> ac_cv_prog_CPP=/opt/intel/cc/10.1.018/bin/icpc
> ac_cv_prog_CXXCPP='/opt/intel/cc/10.1.018/bin/icpc -E'
> ac_cv_prog_ac_ct_AR=ar
> ac_cv_prog_ac_ct_CC=/opt/intel/cc/10.1.018/bin/icc
> ac_cv_prog_ac_ct_OBJDUMP=objdump
> ac_cv_prog_ac_ct_RANLIB=ranlib
> ac_cv_prog_ac_ct_STRIP=strip
> ac_cv_prog_cc_c89=
> ac_cv_prog_cc_g=yes
> ac_cv_prog_cxx_g=yes
> ac_cv_prog_make_make_set=yes
> am_cv_CC_dependencies_compiler_type=gcc3
> am_cv_CXX_dependencies_compiler_type=gcc3
> lt_cv_deplibs_check_method=pass_all
> lt_cv_file_magic_cmd='$MAGIC_CMD'
> lt_cv_file_magic_test_file=
> lt_cv_ld_reload_flag=-r
> lt_cv_nm_interface='BSD nm'
> lt_cv_path_LD=/usr/bin/ld
> lt_cv_path_NM='/usr/bin/nm -B'
> lt_cv_prog_gnu_ld=yes
> lt_cv_sys_global_symbol_pipe='sed -n -e '\''s/^.*[
> ]\([ABCDGIRSTW][ABCDGIRSTW]*\)[         ][
>  ]*\([_A-Za-z][_A-Za-z0-9]*\)$/\1 \2 \2/p'\'''
> lt_cv_sys_global_symbol_to_c_name_address='sed -n -e '\''s/^: \([^ ]*\) $/
>  {\"\1\", (void *) 0},/p'\'' -e '\''s/^[ABCDGIRSTW]* \([^ ]*\) \([^ ]*\)$/
>  {"\2", (void *) \&\2},/p'\'''
> lt_cv_sys_global_symbol_to_c_name_address_lib_prefix='sed -n -e '\''s/^:
> \([^ ]*\) $/  {\"\1\", (void *) 0},/p'\'' -e '\''s/^[ABCDGIRSTW]* \([^ ]*\)
> \(lib[^ ]*\)$/  {"\2", (void *) \&\2},/p'\'' -e '\''s/^[ABCDGIRSTW]* \([^
> ]*\) \([^ ]*\)$/  {"lib\2", (void *) \&\2},/p'\'''
> lt_cv_sys_global_symbol_to_cdecl='sed -n -e '\''s/^T .* \(.*\)$/extern int
> \1();/p'\'' -e '\''s/^[ABCDGIRSTW]* .* \(.*\)$/extern char \1;/p'\'''
> lt_cv_sys_max_cmd_len=98304
>
> ## ----------------- ##
> ## Output variables. ##
> ## ----------------- ##
>
> ACLOCAL='${SHELL} /home/ofer4/Downloads/openbabel-2.2.3/missing --run
> aclocal-1.11'
> AMDEPBACKSLASH='\'
> AMDEP_FALSE='#'
> AMDEP_TRUE=''
> AMTAR='${SHELL} /home/ofer4/Downloads/openbabel-2.2.3/missing --run tar'
> AR='ar'
> AS='as'
> AUTOCONF='sleep 9 ; true || autoconf || skipped'
> AUTOHEADER='sleep 9 ; true || autoheader || skipped'
> AUTOMAKE='sleep 9 ; true || automake || skipped'
> AWK='gawk'
> BIN2HEX_FALSE='#'
> BIN2HEX_TRUE=''
> BOOST_CPPFLAGS='-I/usr/include'
> BOOST_LDFLAGS='-L/usr/lib'
> BUILD_CSHARP_FALSE='#'
> BUILD_CSHARP_TRUE=''
> BUILD_DOCS_FALSE='#'
> BUILD_DOCS_TRUE=''
> BUILD_INCHI_FALSE=''
> BUILD_INCHI_TRUE=''
> BUILD_JAVA_FALSE=''
> BUILD_JAVA_TRUE='#'
> BUILD_PCH_FALSE=''
> BUILD_PCH_TRUE=''
> BUILD_RUBY_FALSE='#'
> BUILD_RUBY_TRUE=''
> BUILD_SCRIPTS_FALSE='#'
> BUILD_SCRIPTS_TRUE=''
> BUILD_SHARED_FALSE=''
> BUILD_SHARED_TRUE=''
> BUILD_SHARED_UNIX_FALSE=''
> BUILD_SHARED_UNIX_TRUE=''
> BUILD_SHARED_WIN_FALSE=''
> BUILD_SHARED_WIN_TRUE=''
> BUILD_SWIG_FALSE=''
> BUILD_SWIG_TRUE='#'
> BUILD_WXGUI_FALSE=''
> BUILD_WXGUI_TRUE='#'
> BUILD_XML_FALSE=''
> BUILD_XML_TRUE=''
> BUILD_ZLIB_FALSE=''
> BUILD_ZLIB_TRUE=''
> CC='/opt/intel/cc/10.1.018/bin/icc'
> CCDEPMODE='depmode=gcc3'
> CFLAGS='-g -O2'
> CPP='/opt/intel/cc/10.1.018/bin/icpc'
> CPPFLAGS=''
> CSHARP='mcs'
> CXX='/opt/intel/cc/10.1.018/bin/icpc'
> CXXCPP='/opt/intel/cc/10.1.018/bin/icpc -E'
> CXXDEPMODE='depmode=gcc3'
> CXXFLAGS='-g -O2'
> CYGPATH_W='echo'
> DEFS=''
> DEPDIR='.deps'
> DLLTOOL='dlltool'
> DOXYGEN='/usr/bin/doxygen'
> DSYMUTIL=''
> DUMPBIN=''
> ECHO_C=''
> ECHO_N='-n'
> ECHO_T=''
> EGREP='/bin/grep -E'
> EXEEXT=''
> FGREP='/bin/grep -F'
> GREP='/bin/grep'
> HAVE_REGEX_FALSE=''
> HAVE_REGEX_TRUE=''
> HAVE_SHARED_POINTER_FALSE=''
> HAVE_SHARED_POINTER_TRUE=''
> INSTALL_DATA='${INSTALL} -m 644'
> INSTALL_PROGRAM='${INSTALL}'
> INSTALL_SCRIPT='${INSTALL}'
> INSTALL_STRIP_PROGRAM='$(install_sh) -c -s'
> JAR=''
> JAVAC=''
> LD='/usr/bin/ld'
> LDFLAGS=''
> LIBDL=''
> LIBOBJS=''
> LIBS=''
> LIBTOOL=''
> LIPO=''
> LN_S='ln -s'
> LTLIBOBJS=''
> MAINT='#'
> MAINTAINER_MODE_FALSE=''
> MAINTAINER_MODE_TRUE='#'
> MAKEINFO='${SHELL} /home/ofer4/Downloads/openbabel-2.2.3/missing --run
> makeinfo'
> MKDIR_P='/bin/mkdir -p'
> NM='/usr/bin/nm -B'
> NMEDIT=''
> OBJDUMP='objdump'
> OBJEXT='o'
> OTOOL64=''
> OTOOL=''
> PACKAGE='openbabel'
> PACKAGE_BUGREPORT='[hidden email]'
> PACKAGE_NAME='Open Babel'
> PACKAGE_STRING='Open Babel 2.2.3'
> PACKAGE_TARNAME='openbabel'
> PACKAGE_VERSION='2.2.3'
> PATH_SEPARATOR=':'
> PERL='/usr/bin/perl'
> PERL_TESTS_FALSE='#'
> PERL_TESTS_TRUE=''
> PROVE='/usr/bin/prove'
> PYTHON='/usr/bin/python'
> RANLIB='ranlib'
> RUBY='/usr/bin/ruby'
> SED='/bin/sed'
> SET_MAKE=''
> SHELL='/bin/bash'
> STRIP='strip'
> SWIG=''
> USE_BOOST_FLAGS_FALSE=''
> USE_BOOST_FLAGS_TRUE=''
> VERSION='2.2.3'
> WXCONFIG='/usr/local/bin/wx-config'
> WX_CPPFLAGS=''
> WX_CXXFLAGS=''
> WX_LIBS=''
> XML2_CONFIG=''
> XML_CPPFLAGS=''
> XML_LIBS=''
> ac_ct_CC='/opt/intel/cc/10.1.018/bin/icc'
> ac_ct_CXX=''
> ac_ct_DUMPBIN=''
> am__EXEEXT_FALSE=''
> am__EXEEXT_TRUE=''
> am__fastdepCC_FALSE='#'
> am__fastdepCC_TRUE=''
> am__fastdepCXX_FALSE='#'
> am__fastdepCXX_TRUE=''
> am__include='include'
> am__isrc=''
> am__leading_dot='.'
> am__quote=''
> am__tar='${AMTAR} chof - "$$tardir"'
> am__untar='${AMTAR} xf -'
> bindir='${exec_prefix}/bin'
> build='i686-pc-linux-gnu'
> build_alias=''
> build_cpu='i686'
> build_os='linux-gnu'
> build_vendor='pc'
> datadir='${datarootdir}'
> datarootdir='${prefix}/share'
> docdir='${datarootdir}/doc/${PACKAGE_TARNAME}'
> dvidir='${docdir}'
> exec_prefix='${prefix}'
> host='i686-pc-linux-gnu'
> host_alias=''
> host_cpu='i686'
> host_os='linux-gnu'
> host_vendor='pc'
> htmldir='${docdir}'
> includedir='${prefix}/include'
> infodir='${datarootdir}/info'
> install_sh='${SHELL} /home/ofer4/Downloads/openbabel-2.2.3/install-sh'
> libdir='${exec_prefix}/lib'
> libexecdir='${exec_prefix}/libexec'
> localedir='${datarootdir}/locale'
> localstatedir='${prefix}/var'
> lt_ECHO='echo'
> mandir='${datarootdir}/man'
> mkdir_p='/bin/mkdir -p'
> oldincludedir='/usr/include'
> pdfdir='${docdir}'
> pkglibdir=''
> prefix='/usr/local'
> 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 "Open Babel"
> #define PACKAGE_TARNAME "openbabel"
> #define PACKAGE_VERSION "2.2.3"
> #define PACKAGE_STRING "Open Babel 2.2.3"
> #define PACKAGE_BUGREPORT "[hidden email]"
> #define BABEL_VERSION "2.2.3"
> #define BABEL_DATADIR "/usr/local/share/openbabel"
> #define HAVE_BOOST /**/
>
> configure: exit 1
>
> ------------------------------------------------------------------------------
>
> _______________________________________________
> OpenBabel-discuss mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>
>

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Re: compilation error using icpc

Noel O'Boyle
Administrator
I also note that configure thinks you are using the GNU compiler.

checking whether we are using the GNU C++ compiler
configure:4965: result: yes

I don't know how to debug this, but you should make sure that the
directory containing all of the intel compiler stuff is at the front
of the path. You may need to specify the compiler explicity with
CXX_FLAGS and so forth (google for the info on specifying the compiler
as I am not sure of the specifics).

- Noel

On 6 May 2010 09:33, Noel O'Boyle <[hidden email]> wrote:

> Hi Ryan,
>
> I see you're using Intel Compiler 10.1.018. I have compiled OB with
> Intel Compiler 11.1.059 without problem (and without BOOST). Do you
> have access to a newer compiler, or even to gcc?
>
> - Noel
>
> On 28 April 2010 23:34, Ryan P. Steele <[hidden email]> wrote:
>> Hi, folks -
>>
>> Having a heck of a time getting openbabel installed.  I installed the boost
>> libraries and finally got those errors corrected.  Now I'm stuck on one that
>> doesn't appear obvious (to me, at least).  My C compiler (Intel icpc) is
>> failing the sanity check during "configure".  My config.log is attached.
>>  Thoughts?  I have no problem compiling other programs with this compiler.
>>
>> Thanks -
>> Ryan
>>
>>
>>
>>
>> This file contains any messages produced by compilers while
>> running configure, to aid debugging if configure makes a mistake.
>>
>> It was created by Open Babel configure 2.2.3, which was
>> generated by GNU Autoconf 2.63.  Invocation command line was
>>
>>  $ ./configure
>>
>> ## --------- ##
>> ## Platform. ##
>> ## --------- ##
>>
>> hostname = ofer4-laptop
>> uname -m = i686
>> uname -r = 2.6.24-22-generic
>> uname -s = Linux
>> uname -v = #1 SMP Mon Nov 24 18:32:42 UTC 2008
>>
>> /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: .
>> PATH: /usr
>> PATH: /usr/bin
>> PATH: /usr/lib/qt4/bin
>> PATH: /usr/local
>> PATH: /usr/local/bin
>> PATH: /bin
>> PATH: /home/ofer4
>> PATH: /opt/intel
>> PATH: /opt/intel/fc/10.1.018
>> PATH: /opt/intel/fc/10.1.018/bin
>> PATH: /opt/intel/cc/10.1.018/bin
>> PATH: /usr/local/texlive/2008/bin/i386-linux
>> PATH: /home/ofer4/mybin
>> PATH: /usr/local/Trolltech/Qt-4.6.2/bin
>> PATH: /usr/local/sbin
>> PATH: /usr/local/bin
>> PATH: /usr/sbin
>> PATH: /usr/bin
>> PATH: /sbin
>> PATH: /bin
>> PATH: /usr/games
>> PATH: /home/ofer4/qchem/bin/perl
>> PATH: /home/ofer4/qchem/bin
>> PATH: /home/ofer4/qchem/gbin
>> PATH: /home/ofer4/qchem/exe
>> PATH: /home/ofer4/qchem/util
>>
>>
>> ## ----------- ##
>> ## Core tests. ##
>> ## ----------- ##
>>
>> configure:2174: checking for a BSD-compatible install
>> configure:2242: result: /usr/bin/install -c
>> configure:2253: checking whether build environment is sane
>> configure:2313: result: yes
>> configure:2454: checking for a thread-safe mkdir -p
>> configure:2493: result: /bin/mkdir -p
>> configure:2506: checking for gawk
>> configure:2522: found /usr/bin/gawk
>> configure:2533: result: gawk
>> configure:2544: checking whether make sets $(MAKE)
>> configure:2566: result: yes
>> configure:2640: checking whether to enable maintainer-specific portions of
>> Makefiles
>> configure:2649: result: no
>> configure:2662: checking auto silent in maintainer mode
>> configure:2674: result: auto-sleep-9
>> configure:2729: checking build system type
>> configure:2747: result: i686-pc-linux-gnu
>> configure:2769: checking host system type
>> configure:2784: result: i686-pc-linux-gnu
>> configure:2883: checking for style of include used by make
>> configure:2911: result: GNU
>> configure:3045: checking for C++ compiler version
>> configure:3053: /opt/intel/cc/10.1.018/bin/icpc --version >&5
>> icpc (ICC) 10.1 20080801
>> Copyright (C) 1985-2008 Intel Corporation.  All rights reserved.
>>
>> configure:3057: $? = 0
>> configure:3064: /opt/intel/cc/10.1.018/bin/icpc -v >&5
>> Version 10.1
>> configure:3068: $? = 0
>> configure:3075: /opt/intel/cc/10.1.018/bin/icpc -V >&5
>> Intel(R) C++ Compiler for applications running on IA-32, Version 10.1
>>  Build 20080801 Package ID: l_cc_p_10.1.018
>> Copyright (C) 1985-2008 Intel Corporation.  All rights reserved.
>> FOR NON-COMMERCIAL USE ONLY
>>
>> configure:3079: $? = 0
>> configure:3102: checking for C++ compiler default output file name
>> configure:3124: /opt/intel/cc/10.1.018/bin/icpc    conftest.cpp  >&5
>> configure:3128: $? = 0
>> configure:3166: result: a.out
>> configure:3185: checking whether the C++ compiler works
>> configure:3195: ./a.out
>> configure:3199: $? = 0
>> configure:3218: result: yes
>> configure:3225: checking whether we are cross compiling
>> configure:3227: result: no
>> configure:3230: checking for suffix of executables
>> configure:3237: /opt/intel/cc/10.1.018/bin/icpc -o conftest    conftest.cpp
>>  >&5
>> configure:3241: $? = 0
>> configure:3267: result:
>> configure:3273: checking for suffix of object files
>> configure:3299: /opt/intel/cc/10.1.018/bin/icpc -c   conftest.cpp >&5
>> configure:3303: $? = 0
>> configure:3328: result: o
>> configure:3332: checking whether we are using the GNU C++ compiler
>> configure:3361: /opt/intel/cc/10.1.018/bin/icpc -c   conftest.cpp >&5
>> configure:3368: $? = 0
>> configure:3385: result: yes
>> configure:3394: checking whether /opt/intel/cc/10.1.018/bin/icpc accepts -g
>> configure:3424: /opt/intel/cc/10.1.018/bin/icpc -c -g  conftest.cpp >&5
>> configure:3431: $? = 0
>> configure:3532: result: yes
>> configure:3557: checking dependency style of /opt/intel/cc/10.1.018/bin/icpc
>> configure:3667: result: gcc3
>> configure:3713: checking for boostlib >= 1.33.1
>> configure:3773: /opt/intel/cc/10.1.018/bin/icpc -c -g -O2  -I/usr/include
>> conftest.cpp >&5
>> configure:3780: $? = 0
>> configure:3786: result: yes
>> configure:4001: checking for gcc
>> configure:4028: result: /opt/intel/cc/10.1.018/bin/icc
>> configure:4260: checking for C compiler version
>> configure:4268: /opt/intel/cc/10.1.018/bin/icc --version >&5
>> icc (ICC) 10.1 20080801
>> Copyright (C) 1985-2008 Intel Corporation.  All rights reserved.
>>
>> configure:4272: $? = 0
>> configure:4279: /opt/intel/cc/10.1.018/bin/icc -v >&5
>> Version 10.1
>> configure:4283: $? = 0
>> configure:4290: /opt/intel/cc/10.1.018/bin/icc -V >&5
>> Intel(R) C Compiler for applications running on IA-32, Version 10.1    Build
>> 20080801 Package ID: l_cc_p_10.1.018
>> Copyright (C) 1985-2008 Intel Corporation.  All rights reserved.
>> FOR NON-COMMERCIAL USE ONLY
>>
>> configure:4294: $? = 0
>> configure:4297: checking whether we are using the GNU C compiler
>> configure:4326: /opt/intel/cc/10.1.018/bin/icc -c   conftest.c >&5
>> configure:4333: $? = 0
>> configure:4350: result: yes
>> configure:4359: checking whether /opt/intel/cc/10.1.018/bin/icc accepts -g
>> configure:4389: /opt/intel/cc/10.1.018/bin/icc -c -g  conftest.c >&5
>> configure:4396: $? = 0
>> configure:4497: result: yes
>> configure:4514: checking for /opt/intel/cc/10.1.018/bin/icc option to accept
>> ISO C89
>> configure:4588: /opt/intel/cc/10.1.018/bin/icc  -c -g -O2  conftest.c >&5
>> configure:4595: $? = 0
>> configure:4618: result: none needed
>> configure:4638: checking dependency style of /opt/intel/cc/10.1.018/bin/icc
>> configure:4748: result: gcc3
>> configure:4875: checking for C++ compiler version
>> configure:4883: /opt/intel/cc/10.1.018/bin/icpc --version >&5
>> icpc (ICC) 10.1 20080801
>> Copyright (C) 1985-2008 Intel Corporation.  All rights reserved.
>>
>> configure:4887: $? = 0
>> configure:4894: /opt/intel/cc/10.1.018/bin/icpc -v >&5
>> Version 10.1
>> configure:4898: $? = 0
>> configure:4905: /opt/intel/cc/10.1.018/bin/icpc -V >&5
>> Intel(R) C++ Compiler for applications running on IA-32, Version 10.1
>>  Build 20080801 Package ID: l_cc_p_10.1.018
>> Copyright (C) 1985-2008 Intel Corporation.  All rights reserved.
>> FOR NON-COMMERCIAL USE ONLY
>>
>> configure:4909: $? = 0
>> configure:4912: checking whether we are using the GNU C++ compiler
>> configure:4965: result: yes
>> configure:4974: checking whether /opt/intel/cc/10.1.018/bin/icpc accepts -g
>> configure:5112: result: yes
>> configure:5137: checking dependency style of /opt/intel/cc/10.1.018/bin/icpc
>> configure:5247: result: gcc3
>> configure:5267: checking how to run the C++ preprocessor
>> configure:5303: /opt/intel/cc/10.1.018/bin/icpc -E  conftest.cpp
>> configure:5310: $? = 0
>> configure:5341: /opt/intel/cc/10.1.018/bin/icpc -E  conftest.cpp
>> conftest.cpp(11): error #5: could not open source file "ac_nonexistent.h"
>>  #include <ac_nonexistent.h>
>>                             ^
>>
>> configure:5348: $? = 2
>> configure: failed program was:
>> | /* confdefs.h.  */
>> | #define PACKAGE_NAME "Open Babel"
>> | #define PACKAGE_TARNAME "openbabel"
>> | #define PACKAGE_VERSION "2.2.3"
>> | #define PACKAGE_STRING "Open Babel 2.2.3"
>> | #define PACKAGE_BUGREPORT "[hidden email]"
>> | #define BABEL_VERSION "2.2.3"
>> | #define BABEL_DATADIR "/usr/local/share/openbabel"
>> | #define HAVE_BOOST /**/
>> | /* end confdefs.h.  */
>> | #include <ac_nonexistent.h>
>> configure:5381: result: /opt/intel/cc/10.1.018/bin/icpc -E
>> configure:5410: /opt/intel/cc/10.1.018/bin/icpc -E  conftest.cpp
>> configure:5417: $? = 0
>> configure:5448: /opt/intel/cc/10.1.018/bin/icpc -E  conftest.cpp
>> conftest.cpp(11): error #5: could not open source file "ac_nonexistent.h"
>>  #include <ac_nonexistent.h>
>>                             ^
>>
>> configure:5455: $? = 2
>> configure: failed program was:
>> | /* confdefs.h.  */
>> | #define PACKAGE_NAME "Open Babel"
>> | #define PACKAGE_TARNAME "openbabel"
>> | #define PACKAGE_VERSION "2.2.3"
>> | #define PACKAGE_STRING "Open Babel 2.2.3"
>> | #define PACKAGE_BUGREPORT "[hidden email]"
>> | #define BABEL_VERSION "2.2.3"
>> | #define BABEL_DATADIR "/usr/local/share/openbabel"
>> | #define HAVE_BOOST /**/
>> | /* end confdefs.h.  */
>> | #include <ac_nonexistent.h>
>> configure:5508: checking for a BSD-compatible install
>> configure:5576: result: /usr/bin/install -c
>> configure:5589: checking for doxygen
>> configure:5607: found /usr/bin/doxygen
>> configure:5619: result: /usr/bin/doxygen
>> configure:5629: checking for swig
>> configure:5662: result: no
>> configure:5669: checking for perl
>> configure:5687: found /usr/bin/perl
>> configure:5699: result: /usr/bin/perl
>> configure:5709: checking for prove
>> configure:5727: found /usr/bin/prove
>> configure:5739: result: /usr/bin/prove
>> configure:5749: checking for python
>> configure:5767: found /usr/bin/python
>> configure:5779: result: /usr/bin/python
>> configure:5789: checking for ruby
>> configure:5807: found /usr/bin/ruby
>> configure:5819: result: /usr/bin/ruby
>> configure:5831: checking for gmcs
>> configure:5864: result: no
>> configure:5875: checking for javac
>> configure:5908: result: no
>> configure:5915: checking for jar
>> configure:5948: result: no
>> configure:5958: checking for wx-config
>> configure:5976: found /usr/local/bin/wx-config
>> configure:5988: result: /usr/local/bin/wx-config
>> configure:6443: checking for a sed that does not truncate output
>> configure:6509: result: /bin/sed
>> configure:6527: checking for grep that handles long lines and -e
>> configure:6587: result: /bin/grep
>> configure:6592: checking for egrep
>> configure:6656: result: /bin/grep -E
>> configure:6661: checking for fgrep
>> configure:6725: result: /bin/grep -F
>> configure:6760: checking for ld used by /opt/intel/cc/10.1.018/bin/icc
>> configure:6827: result: /usr/bin/ld
>> configure:6836: checking if the linker (/usr/bin/ld) is GNU ld
>> configure:6851: result: yes
>> configure:6863: checking for BSD- or MS-compatible name lister (nm)
>> configure:6912: result: /usr/bin/nm -B
>> configure:7030: checking the name lister (/usr/bin/nm -B) interface
>> configure:7037: /opt/intel/cc/10.1.018/bin/icc -c -g -O2  conftest.c >&5
>> configure:7040: /usr/bin/nm -B "conftest.o"
>> configure:7043: output
>> 00000000 N .debug_info_seg
>> 00000000 B some_variable
>> configure:7050: result: BSD nm
>> configure:7053: checking whether ln -s works
>> configure:7057: result: yes
>> configure:7065: checking the maximum length of command line arguments
>> configure:7185: result: 98304
>> configure:7202: checking whether the shell understands some XSI constructs
>> configure:7212: result: yes
>> configure:7216: checking whether the shell understands "+="
>> configure:7222: result: yes
>> configure:7257: checking for /usr/bin/ld option to reload object files
>> configure:7264: result: -r
>> configure:7333: checking for objdump
>> configure:7360: result: objdump
>> configure:7389: checking how to recognize dependent libraries
>> configure:7585: result: pass_all
>> configure:7645: checking for ar
>> configure:7661: found /usr/bin/ar
>> configure:7672: result: ar
>> configure:7750: checking for strip
>> configure:7766: found /usr/bin/strip
>> configure:7777: result: strip
>> configure:7849: checking for ranlib
>> configure:7865: found /usr/bin/ranlib
>> configure:7876: result: ranlib
>> configure:7966: checking command to parse /usr/bin/nm -B output from
>> /opt/intel/cc/10.1.018/bin/icc object
>> configure:8084: /opt/intel/cc/10.1.018/bin/icc -c -g -O2  conftest.c >&5
>> configure:8087: $? = 0
>> configure:8091: /usr/bin/nm -B conftest.o \| sed -n -e 's/^.*[
>> ]\([ABCDGIRSTW][ABCDGIRSTW]*\)[         ][
>>  ]*\([_A-Za-z][_A-Za-z0-9]*\)$/\1 \2 \2/p' \> conftest.nm
>> configure:8094: $? = 0
>> configure:8148: /opt/intel/cc/10.1.018/bin/icc -o conftest -g -O2
>> conftest.c conftstm.o >&5
>> configure:8151: $? = 0
>> configure:8189: result: ok
>> configure:9056: checking how to run the C preprocessor
>> configure:9174: result: /opt/intel/cc/10.1.018/bin/icpc
>> configure:9203: /opt/intel/cc/10.1.018/bin/icpc  conftest.c
>> conftest.c(16): error: identifier "Syntax" is undefined
>>                     Syntax error
>>                     ^
>>
>> conftest.c(16): error: expected a ";"
>>
>> compilation aborted for conftest.c (code 2)
>> configure:9210: $? = 2
>> configure: failed program was:
>> | /* confdefs.h.  */
>> | #define PACKAGE_NAME "Open Babel"
>> | #define PACKAGE_TARNAME "openbabel"
>> | #define PACKAGE_VERSION "2.2.3"
>> | #define PACKAGE_STRING "Open Babel 2.2.3"
>> | #define PACKAGE_BUGREPORT "[hidden email]"
>> | #define BABEL_VERSION "2.2.3"
>> | #define BABEL_DATADIR "/usr/local/share/openbabel"
>> | #define HAVE_BOOST /**/
>> | /* end confdefs.h.  */
>> | #ifdef __STDC__
>> | # include <limits.h>
>> | #else
>> | # include <assert.h>
>> | #endif
>> |                    Syntax error
>> configure:9203: /opt/intel/cc/10.1.018/bin/icpc  conftest.c
>> conftest.c(16): error: identifier "Syntax" is undefined
>>                     Syntax error
>>                     ^
>>
>> conftest.c(16): error: expected a ";"
>>
>> compilation aborted for conftest.c (code 2)
>> configure:9210: $? = 2
>> configure: failed program was:
>> | /* confdefs.h.  */
>> | #define PACKAGE_NAME "Open Babel"
>> | #define PACKAGE_TARNAME "openbabel"
>> | #define PACKAGE_VERSION "2.2.3"
>> | #define PACKAGE_STRING "Open Babel 2.2.3"
>> | #define PACKAGE_BUGREPORT "[hidden email]"
>> | #define BABEL_VERSION "2.2.3"
>> | #define BABEL_DATADIR "/usr/local/share/openbabel"
>> | #define HAVE_BOOST /**/
>> | /* end confdefs.h.  */
>> | #ifdef __STDC__
>> | # include <limits.h>
>> | #else
>> | # include <assert.h>
>> | #endif
>> |                    Syntax error
>> configure:9272: error: in `/home/ofer4/Downloads/openbabel-2.2.3':
>> configure:9275: error: C preprocessor "/opt/intel/cc/10.1.018/bin/icpc"
>> fails sanity check
>> See `config.log' for more details.
>>
>> ## ---------------- ##
>> ## Cache variables. ##
>> ## ---------------- ##
>>
>> ac_cv_build=i686-pc-linux-gnu
>> ac_cv_c_compiler_gnu=yes
>> ac_cv_cxx_compiler_gnu=yes
>> ac_cv_env_CCC_set=
>> ac_cv_env_CCC_value=
>> ac_cv_env_CC_set=set
>> ac_cv_env_CC_value=/opt/intel/cc/10.1.018/bin/icc
>> 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=set
>> ac_cv_env_CPP_value=/opt/intel/cc/10.1.018/bin/icpc
>> 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=set
>> ac_cv_env_CXX_value=/opt/intel/cc/10.1.018/bin/icpc
>> ac_cv_env_LDFLAGS_set=
>> ac_cv_env_LDFLAGS_value=
>> ac_cv_env_LIBS_set=
>> ac_cv_env_LIBS_value=
>> ac_cv_env_WXCONFIG_set=
>> ac_cv_env_WXCONFIG_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=i686-pc-linux-gnu
>> ac_cv_objext=o
>> ac_cv_path_DOXYGEN=/usr/bin/doxygen
>> ac_cv_path_EGREP='/bin/grep -E'
>> ac_cv_path_FGREP='/bin/grep -F'
>> ac_cv_path_GREP=/bin/grep
>> ac_cv_path_PERL=/usr/bin/perl
>> ac_cv_path_PROVE=/usr/bin/prove
>> ac_cv_path_PYTHON=/usr/bin/python
>> ac_cv_path_RUBY=/usr/bin/ruby
>> ac_cv_path_SED=/bin/sed
>> ac_cv_path_WXCONFIG=/usr/local/bin/wx-config
>> ac_cv_path_install='/usr/bin/install -c'
>> ac_cv_path_mkdir=/bin/mkdir
>> ac_cv_prog_AWK=gawk
>> ac_cv_prog_CPP=/opt/intel/cc/10.1.018/bin/icpc
>> ac_cv_prog_CXXCPP='/opt/intel/cc/10.1.018/bin/icpc -E'
>> ac_cv_prog_ac_ct_AR=ar
>> ac_cv_prog_ac_ct_CC=/opt/intel/cc/10.1.018/bin/icc
>> ac_cv_prog_ac_ct_OBJDUMP=objdump
>> ac_cv_prog_ac_ct_RANLIB=ranlib
>> ac_cv_prog_ac_ct_STRIP=strip
>> ac_cv_prog_cc_c89=
>> ac_cv_prog_cc_g=yes
>> ac_cv_prog_cxx_g=yes
>> ac_cv_prog_make_make_set=yes
>> am_cv_CC_dependencies_compiler_type=gcc3
>> am_cv_CXX_dependencies_compiler_type=gcc3
>> lt_cv_deplibs_check_method=pass_all
>> lt_cv_file_magic_cmd='$MAGIC_CMD'
>> lt_cv_file_magic_test_file=
>> lt_cv_ld_reload_flag=-r
>> lt_cv_nm_interface='BSD nm'
>> lt_cv_path_LD=/usr/bin/ld
>> lt_cv_path_NM='/usr/bin/nm -B'
>> lt_cv_prog_gnu_ld=yes
>> lt_cv_sys_global_symbol_pipe='sed -n -e '\''s/^.*[
>> ]\([ABCDGIRSTW][ABCDGIRSTW]*\)[         ][
>>  ]*\([_A-Za-z][_A-Za-z0-9]*\)$/\1 \2 \2/p'\'''
>> lt_cv_sys_global_symbol_to_c_name_address='sed -n -e '\''s/^: \([^ ]*\) $/
>>  {\"\1\", (void *) 0},/p'\'' -e '\''s/^[ABCDGIRSTW]* \([^ ]*\) \([^ ]*\)$/
>>  {"\2", (void *) \&\2},/p'\'''
>> lt_cv_sys_global_symbol_to_c_name_address_lib_prefix='sed -n -e '\''s/^:
>> \([^ ]*\) $/  {\"\1\", (void *) 0},/p'\'' -e '\''s/^[ABCDGIRSTW]* \([^ ]*\)
>> \(lib[^ ]*\)$/  {"\2", (void *) \&\2},/p'\'' -e '\''s/^[ABCDGIRSTW]* \([^
>> ]*\) \([^ ]*\)$/  {"lib\2", (void *) \&\2},/p'\'''
>> lt_cv_sys_global_symbol_to_cdecl='sed -n -e '\''s/^T .* \(.*\)$/extern int
>> \1();/p'\'' -e '\''s/^[ABCDGIRSTW]* .* \(.*\)$/extern char \1;/p'\'''
>> lt_cv_sys_max_cmd_len=98304
>>
>> ## ----------------- ##
>> ## Output variables. ##
>> ## ----------------- ##
>>
>> ACLOCAL='${SHELL} /home/ofer4/Downloads/openbabel-2.2.3/missing --run
>> aclocal-1.11'
>> AMDEPBACKSLASH='\'
>> AMDEP_FALSE='#'
>> AMDEP_TRUE=''
>> AMTAR='${SHELL} /home/ofer4/Downloads/openbabel-2.2.3/missing --run tar'
>> AR='ar'
>> AS='as'
>> AUTOCONF='sleep 9 ; true || autoconf || skipped'
>> AUTOHEADER='sleep 9 ; true || autoheader || skipped'
>> AUTOMAKE='sleep 9 ; true || automake || skipped'
>> AWK='gawk'
>> BIN2HEX_FALSE='#'
>> BIN2HEX_TRUE=''
>> BOOST_CPPFLAGS='-I/usr/include'
>> BOOST_LDFLAGS='-L/usr/lib'
>> BUILD_CSHARP_FALSE='#'
>> BUILD_CSHARP_TRUE=''
>> BUILD_DOCS_FALSE='#'
>> BUILD_DOCS_TRUE=''
>> BUILD_INCHI_FALSE=''
>> BUILD_INCHI_TRUE=''
>> BUILD_JAVA_FALSE=''
>> BUILD_JAVA_TRUE='#'
>> BUILD_PCH_FALSE=''
>> BUILD_PCH_TRUE=''
>> BUILD_RUBY_FALSE='#'
>> BUILD_RUBY_TRUE=''
>> BUILD_SCRIPTS_FALSE='#'
>> BUILD_SCRIPTS_TRUE=''
>> BUILD_SHARED_FALSE=''
>> BUILD_SHARED_TRUE=''
>> BUILD_SHARED_UNIX_FALSE=''
>> BUILD_SHARED_UNIX_TRUE=''
>> BUILD_SHARED_WIN_FALSE=''
>> BUILD_SHARED_WIN_TRUE=''
>> BUILD_SWIG_FALSE=''
>> BUILD_SWIG_TRUE='#'
>> BUILD_WXGUI_FALSE=''
>> BUILD_WXGUI_TRUE='#'
>> BUILD_XML_FALSE=''
>> BUILD_XML_TRUE=''
>> BUILD_ZLIB_FALSE=''
>> BUILD_ZLIB_TRUE=''
>> CC='/opt/intel/cc/10.1.018/bin/icc'
>> CCDEPMODE='depmode=gcc3'
>> CFLAGS='-g -O2'
>> CPP='/opt/intel/cc/10.1.018/bin/icpc'
>> CPPFLAGS=''
>> CSHARP='mcs'
>> CXX='/opt/intel/cc/10.1.018/bin/icpc'
>> CXXCPP='/opt/intel/cc/10.1.018/bin/icpc -E'
>> CXXDEPMODE='depmode=gcc3'
>> CXXFLAGS='-g -O2'
>> CYGPATH_W='echo'
>> DEFS=''
>> DEPDIR='.deps'
>> DLLTOOL='dlltool'
>> DOXYGEN='/usr/bin/doxygen'
>> DSYMUTIL=''
>> DUMPBIN=''
>> ECHO_C=''
>> ECHO_N='-n'
>> ECHO_T=''
>> EGREP='/bin/grep -E'
>> EXEEXT=''
>> FGREP='/bin/grep -F'
>> GREP='/bin/grep'
>> HAVE_REGEX_FALSE=''
>> HAVE_REGEX_TRUE=''
>> HAVE_SHARED_POINTER_FALSE=''
>> HAVE_SHARED_POINTER_TRUE=''
>> INSTALL_DATA='${INSTALL} -m 644'
>> INSTALL_PROGRAM='${INSTALL}'
>> INSTALL_SCRIPT='${INSTALL}'
>> INSTALL_STRIP_PROGRAM='$(install_sh) -c -s'
>> JAR=''
>> JAVAC=''
>> LD='/usr/bin/ld'
>> LDFLAGS=''
>> LIBDL=''
>> LIBOBJS=''
>> LIBS=''
>> LIBTOOL=''
>> LIPO=''
>> LN_S='ln -s'
>> LTLIBOBJS=''
>> MAINT='#'
>> MAINTAINER_MODE_FALSE=''
>> MAINTAINER_MODE_TRUE='#'
>> MAKEINFO='${SHELL} /home/ofer4/Downloads/openbabel-2.2.3/missing --run
>> makeinfo'
>> MKDIR_P='/bin/mkdir -p'
>> NM='/usr/bin/nm -B'
>> NMEDIT=''
>> OBJDUMP='objdump'
>> OBJEXT='o'
>> OTOOL64=''
>> OTOOL=''
>> PACKAGE='openbabel'
>> PACKAGE_BUGREPORT='[hidden email]'
>> PACKAGE_NAME='Open Babel'
>> PACKAGE_STRING='Open Babel 2.2.3'
>> PACKAGE_TARNAME='openbabel'
>> PACKAGE_VERSION='2.2.3'
>> PATH_SEPARATOR=':'
>> PERL='/usr/bin/perl'
>> PERL_TESTS_FALSE='#'
>> PERL_TESTS_TRUE=''
>> PROVE='/usr/bin/prove'
>> PYTHON='/usr/bin/python'
>> RANLIB='ranlib'
>> RUBY='/usr/bin/ruby'
>> SED='/bin/sed'
>> SET_MAKE=''
>> SHELL='/bin/bash'
>> STRIP='strip'
>> SWIG=''
>> USE_BOOST_FLAGS_FALSE=''
>> USE_BOOST_FLAGS_TRUE=''
>> VERSION='2.2.3'
>> WXCONFIG='/usr/local/bin/wx-config'
>> WX_CPPFLAGS=''
>> WX_CXXFLAGS=''
>> WX_LIBS=''
>> XML2_CONFIG=''
>> XML_CPPFLAGS=''
>> XML_LIBS=''
>> ac_ct_CC='/opt/intel/cc/10.1.018/bin/icc'
>> ac_ct_CXX=''
>> ac_ct_DUMPBIN=''
>> am__EXEEXT_FALSE=''
>> am__EXEEXT_TRUE=''
>> am__fastdepCC_FALSE='#'
>> am__fastdepCC_TRUE=''
>> am__fastdepCXX_FALSE='#'
>> am__fastdepCXX_TRUE=''
>> am__include='include'
>> am__isrc=''
>> am__leading_dot='.'
>> am__quote=''
>> am__tar='${AMTAR} chof - "$$tardir"'
>> am__untar='${AMTAR} xf -'
>> bindir='${exec_prefix}/bin'
>> build='i686-pc-linux-gnu'
>> build_alias=''
>> build_cpu='i686'
>> build_os='linux-gnu'
>> build_vendor='pc'
>> datadir='${datarootdir}'
>> datarootdir='${prefix}/share'
>> docdir='${datarootdir}/doc/${PACKAGE_TARNAME}'
>> dvidir='${docdir}'
>> exec_prefix='${prefix}'
>> host='i686-pc-linux-gnu'
>> host_alias=''
>> host_cpu='i686'
>> host_os='linux-gnu'
>> host_vendor='pc'
>> htmldir='${docdir}'
>> includedir='${prefix}/include'
>> infodir='${datarootdir}/info'
>> install_sh='${SHELL} /home/ofer4/Downloads/openbabel-2.2.3/install-sh'
>> libdir='${exec_prefix}/lib'
>> libexecdir='${exec_prefix}/libexec'
>> localedir='${datarootdir}/locale'
>> localstatedir='${prefix}/var'
>> lt_ECHO='echo'
>> mandir='${datarootdir}/man'
>> mkdir_p='/bin/mkdir -p'
>> oldincludedir='/usr/include'
>> pdfdir='${docdir}'
>> pkglibdir=''
>> prefix='/usr/local'
>> 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 "Open Babel"
>> #define PACKAGE_TARNAME "openbabel"
>> #define PACKAGE_VERSION "2.2.3"
>> #define PACKAGE_STRING "Open Babel 2.2.3"
>> #define PACKAGE_BUGREPORT "[hidden email]"
>> #define BABEL_VERSION "2.2.3"
>> #define BABEL_DATADIR "/usr/local/share/openbabel"
>> #define HAVE_BOOST /**/
>>
>> configure: exit 1
>>
>> ------------------------------------------------------------------------------
>>
>> _______________________________________________
>> OpenBabel-discuss mailing list
>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>>
>>
>

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