I can't really tell why this is failing, but my guess would be that the configure script is trying to test your fortran compiler, using g77, but linking against gfortran libraries. I could be wrong, but there is not much information here to work with. These types of problems are usually related to the particular compilers you have installed.
With problems like this it is ALWAYS best to take the path of least resistance rather than trying to figure out how to make the compile work. This may sound intellectually lazy, but, trust me, it is pure wisdom.
What I would do is update X Code to 4.2, then install the latest greatest fink for your system and then do a "fink install coot" which will give you the clipper libraries (and also give you coot as a bonus).
My /sw/etc/fink.conf has this line (which you should probably emulate if you go this route):
Trees: local/main stable/main stable/crypto unstable/main unstable/crypto local/injected
If you already have fink, then you can do this:
fink selfupdate
fink scanpackages
fink update-all
fink install coot
And then you would just use the ccp4 from the .dmg package and the clipper libraries from fink.
Others may have different suggestions as there are about a million ways to skin this cat. My advice is to choose the easiest.
James
On Feb 11, 2012, at 11:31 PM, Rojan Shrestha wrote:
> 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"
> #endif
> #ifdef __cplusplus
> extern "C" void exit (int);
>
> configure: exit 1
