Error while compiling ccp4 source in mac os

From: Rojan Shrestha
Date: 12 February 2012 06:31

Dear all,

 

I would like to compile the CCP4 in mac book pro with intel cpu. The purpose of installing ccp4 using source code is to compile the clipper library.  Although I have already installed ccp4 dmg package provided for  mac os, I could not compile the clipper using ccp4.  The problem occurred due to the g77 fortran library and detail error message is shown below. I have only gfortran as default provided by gnu for Mac OS. I also installed g77 manual but my problem is not still solved.

 

Do you know the solution of this problem?

 

Here is error while configure

checking for Fortran 77 libraries... rm: conftest.dSYM: is a directory

-lcrt1.10.5.o -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin11/4.6.2 -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin11/4.6.2/../../.. -lgfortran -lSystem -lgcc_ext.10.5 -lquadmath -lm

checking for dummy main to link with Fortran libraries... rm: conftest.dSYM: is a directory

unknown

configure: error: linking to Fortran libraries from C fails

See `config.log' for more details.

 

Inside config.log

## ---------------- ##

## Cache variables. ##

## ---------------- ##

 

ac_cv_build=i386-apple-darwin11.2.0

ac_cv_build_alias=i386-apple-darwin11.2.0

ac_cv_c_compiler_gnu=yes

ac_cv_cxx_compiler_gnu=yes

ac_cv_env_CC_set=set

ac_cv_env_CC_value=gcc

ac_cv_env_CFLAGS_set=set

ac_cv_env_CFLAGS_value='-O2 -DGFORTRAN -DPROTOTYPE'

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=set

ac_cv_env_CXX_value=g++

ac_cv_env_F77_set=set

ac_cv_env_F77_value=gfortran

ac_cv_env_FFLAGS_set=

ac_cv_env_FFLAGS_value=

ac_cv_env_LDFLAGS_set=

ac_cv_env_LDFLAGS_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_exeext=

ac_cv_f77_compiler_gnu=yes

ac_cv_f77_dummy_main=unknown

ac_cv_flibs=' -lcrt1.10.5.o -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin11/4.6.2 -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin11/4.6.2/../../.. -lgfortran -lSystem -lgcc_ext.10.5 -lquadmath -lm'

ac_cv_fortran_dummy_main=unknown

ac_cv_header_dlfcn_h=yes

ac_cv_header_inttypes_h=yes

ac_cv_header_memory_h=yes

ac_cv_header_stdc=yes

ac_cv_header_stdint_h=yes

ac_cv_header_stdlib_h=yes

ac_cv_header_string_h=yes

ac_cv_header_strings_h=yes

ac_cv_header_sys_stat_h=yes

ac_cv_header_sys_types_h=yes

ac_cv_header_unistd_h=yes

ac_cv_host=i386-apple-darwin11.2.0

ac_cv_host_alias=i386-apple-darwin11.2.0

ac_cv_objext=o

ac_cv_path_install='/usr/bin/install -c'

ac_cv_prog_AWK=awk

ac_cv_prog_CC=gcc

ac_cv_prog_CPP='gcc -E'

ac_cv_prog_CXXCPP='g++ -E'

ac_cv_prog_PERL=perl

ac_cv_prog_ac_ct_AR=ar

ac_cv_prog_ac_ct_RANLIB=ranlib

ac_cv_prog_ac_ct_STRIP=strip

ac_cv_prog_cc_g=yes

ac_cv_prog_cc_stdc=

ac_cv_prog_cxx_g=yes

ac_cv_prog_egrep='grep -E'

ac_cv_prog_f77_g=yes

ac_cv_prog_f77_v=-v

ac_cv_prog_gcc_2_90=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_objdir=.libs

lt_cv_path_LD=/usr/llvm-gcc-4.2/libexec/gcc/i686-apple-darwin11/4.2.1/ld

lt_cv_path_LDCXX=/usr/llvm-gcc-4.2/libexec/gcc/i686-apple-darwin11/4.2.1/ld

lt_cv_path_NM=/usr/bin/nm

lt_cv_path_SED=/usr/bin/sed

lt_cv_prog_compiler_c_o=yes

lt_cv_prog_compiler_c_o_CXX=yes

lt_cv_prog_compiler_c_o_F77=yes

lt_cv_prog_compiler_rtti_exceptions=no

lt_cv_prog_gnu_ld=no

lt_cv_prog_gnu_ldcxx=no

lt_cv_sys_global_symbol_pipe='sed -n -e '\''s/^.*[          ]\([BCDEGRST][BCDEGRST]*\)[                 ][             ]*_\([_A-Za-z][_A-Za-z0-9]*\)$/\1 _\2 \2/p'\'''

lt_cv_sys_global_symbol_to_c_name_address='sed -n -e '\''s/^: \([^ ]*\) $/  {\"\1\", (lt_ptr) 0},/p'\'' -e '\''s/^[BCDEGRST] \([^ ]*\) \([^ ]*\)$/  {"\2", (lt_ptr) \&\2},/p'\'''

lt_cv_sys_global_symbol_to_cdecl='sed -n -e '\''s/^. .* \(.*\)$/extern int \1;/p'\'''

lt_cv_sys_max_cmd_len=196608

lt_lt_cv_prog_compiler_c_o='"yes"'

lt_lt_cv_prog_compiler_c_o_CXX='"yes"'

lt_lt_cv_prog_compiler_c_o_F77='"yes"'

lt_lt_cv_sys_global_symbol_pipe='"sed -n -e '\''s/^.*[ ]\\([BCDEGRST][BCDEGRST]*\\)[             ][             ]*_\\([_A-Za-z][_A-Za-z0-9]*\\)\$/\\1 _\\2 \\2/p'\''"'

lt_lt_cv_sys_global_symbol_to_c_name_address='"sed -n -e '\''s/^: \\([^ ]*\\) \$/  {\\\"\\1\\\", (lt_ptr) 0},/p'\'' -e '\''s/^[BCDEGRST] \\([^ ]*\\) \\([^ ]*\\)\$/  {\"\\2\", (lt_ptr) \\&\\2},/p'\''"'

lt_lt_cv_sys_global_symbol_to_cdecl='"sed -n -e '\''s/^. .* \\(.*\\)\$/extern int \\1;/p'\''"'

 

## ----------------- ##

## Output variables. ##

## ----------------- ##

 

ACLOCAL='${SHELL} /Users/rojan/Myspace/tmp/clipper_test/ccp4-6.1.1/lib/fftw/missing --run aclocal-1.9'

ALLOCA=''

AMDEPBACKSLASH='\'

AMDEP_FALSE='#'

AMDEP_TRUE=''

AMTAR='${SHELL} /Users/rojan/Myspace/tmp/clipper_test/ccp4-6.1.1/lib/fftw/missing --run tar'

AR='ar'

AUTOCONF='${SHELL} /Users/rojan/Myspace/tmp/clipper_test/ccp4-6.1.1/lib/fftw/missing --run autoconf'

AUTOHEADER='${SHELL} /Users/rojan/Myspace/tmp/clipper_test/ccp4-6.1.1/lib/fftw/missing --run autoheader'

AUTOMAKE='${SHELL} /Users/rojan/Myspace/tmp/clipper_test/ccp4-6.1.1/lib/fftw/missing --run automake-1.9'

AWK='awk'

CC='gcc'

CCDEPMODE='depmode=gcc3'

CFLAGS='-O2 -DGFORTRAN -DPROTOTYPE'

CPP='gcc -E'

CPPFLAGS=''

CXX='g++'

CXXCPP='g++ -E'

CXXDEPMODE='depmode=gcc3'

CXXFLAGS='-g -O2'

CYGPATH_W='echo'

DEFS=''

DEPDIR='.deps'

ECHO='/bin/echo'

ECHO_C='ECHO_N=''

ECHO_T=''

EGREP='grep -E'

EXEEXT=''

F77='gfortran'

FFLAGS='-g -O2'

FFTW_MPI_INCLUDELIST=''

FFTW_MPI_LIBLIST=''

FFTW_MPI_PROGLIST=''

FFTW_PREFIX1='xyz'

FFTW_PREFIX=''

FFTW_THREADS_INCLUDELIST=''

FFTW_THREADS_LIBLIST=''

FFTW_THREADS_PROGLIST=''

FLIBS=' -lcrt1.10.5.o -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin11/4.6.2 -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin11/4.6.2/../../.. -lgfortran -lSystem -lgcc_ext.10.5 -lquadmath -lm'

INSTALL_DATA='cp -p'

INSTALL_PROGRAM='cp -p'

INSTALL_SCRIPT='${INSTALL}'

INSTALL_STRIP_PROGRAM='${SHELL} $(install_sh) -c -s'

LDFLAGS=''

LIBOBJS=''

LIBS=''

LIBTOOL='$(SHELL) $(top_builddir)/libtool'

LN_S='ln -s'

LTLIBOBJS=''

MAKEINFO='${SHELL} /Users/rojan/Myspace/tmp/clipper_test/ccp4-6.1.1/lib/fftw/missing --run makeinfo'

MPICC=''

MPILIBS=''

OBJEXT='o'

PACKAGE='fftw'

PACKAGE_BUGREPORT=''

PACKAGE_NAME=''

PACKAGE_STRING=''

PACKAGE_TARNAME=''

PACKAGE_VERSION=''

PATH_SEPARATOR=':'

PERL='perl'

PTHREAD_CC=''

PTHREAD_CFLAGS=''

PTHREAD_LIBS=''

RANLIB='ranlib'

SED='/usr/bin/sed'

SET_MAKE=''

SHARED_VERSION=''

SHARED_VERSION_INFO='2:7:0'

SHELL='/bin/sh'

STRIP='strip'

THREADLIBS=''

VERSION='2.1.5'

ac_ct_AR='ar'

ac_ct_CC=''

ac_ct_CXX=''

ac_ct_F77=''

ac_ct_RANLIB='ranlib'

ac_ct_STRIP='strip'

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='/Users/rojan/Myspace/tmp/clipper_test/ccp4-6.1.1/bin'

build='i386-apple-darwin11.2.0'

build_alias=''

build_cpu='i386'

build_os='darwin11.2.0'

build_vendor='apple'

datadir='${prefix}/share'

exec_prefix='/Users/rojan/Myspace/tmp/clipper_test/ccp4-6.1.1'

host='i386-apple-darwin11.2.0'

host_alias=''

host_cpu='i386'

host_os='darwin11.2.0'

host_vendor='apple'

includedir='${prefix}/include'

infodir='${prefix}/info'

install_sh='/Users/rojan/Myspace/tmp/clipper_test/ccp4-6.1.1/lib/fftw/install-sh'

libdir='/Users/rojan/Myspace/tmp/clipper_test/ccp4-6.1.1/lib'

libexecdir='${exec_prefix}/libexec'

localstatedir='${prefix}/var'

mandir='${prefix}/man'

mkdir_p='$(mkinstalldirs)'

oldincludedir='/usr/include'

prefix='/Users/rojan/Myspace/tmp/clipper_test/ccp4-6.1.1'

program_transform_name='s,x,x,'

sbindir='${exec_prefix}/sbin'

sharedstatedir='${prefix}/com'

sysconfdir='${prefix}/etc'

target_alias=''

 

## ----------- ##

## confdefs.h. ##

## ----------- ##

 

#define FFTW_ENABLE_FLOAT 1

#define HAVE_DLFCN_H 1

#define HAVE_INTTYPES_H 1

#define HAVE_MEMORY_H 1

#define HAVE_STDINT_H 1

#define HAVE_STDLIB_H 1

#define HAVE_STRINGS_H 1

#define HAVE_STRING_H 1

#define HAVE_SYS_STAT_H 1

#define HAVE_SYS_TYPES_H 1

#define HAVE_UNISTD_H 1

#define PACKAGE "fftw"

#define PACKAGE_BUGREPORT ""

#define PACKAGE_NAME ""

#define PACKAGE_STRING ""

#define PACKAGE_TARNAME ""

#define PACKAGE_VERSION ""

#define STDC_HEADERS 1

#define VERSION "2.1.5"