[Dock-fans] Installing DOCK 6.4 on Mac OSX Snow Leopard

Scott Brozell sbrozell at rci.rutgers.edu
Fri Apr 22 19:44:37 PDT 2011


Hi,

> ../../install/config.h:2: *** missing separator.  Stop.

This might be extraneous tabs in your macro definitions;
remove the whitespace are rebuild.

> I also googled the architecture warning and found the following link (http://www.qtcentre.org/threads/30670-On-Mac-quot-...file-was-built-for-unsupported-file-format..-quot-SOLVED).  Accordingly, I tried editing the /install/config.h file to: 'CC=          gcc -arch i386' and 'CXX=        g++ -arch i386'.  Running 'make all' after the edits above gave the following error:

Another way to get changes into the build process is DOCKBUILDFLAGS:
make DOCKBUILDFLAGS='-arch i386'

scott

On Fri, Apr 22, 2011 at 12:28:05PM -0700, Jennifer Lahti wrote:
> 
> I didn't find any '^M' in the files that I edited (I checked this in vi which will show these characters when inserted with programs such as TextEdit).  Just to make certain, I started over from the beginning (by running 'make distclean') and repeating the configure and make commands.  Without editing the /install/configure.h file (i.e. no chance of accidentally inserting ^M), this is the verbose output I get:
> 
> 
> ~~~~~~~~~~~~~~~~~~~~
> Starting installation of 
> DOCK v6.4
> at Fri Apr 22 11:10:06 PDT 2011.
...
> cd accessories && make install
> g77 -c -O2 -fno-automatic -fno-second-underscore -o showbox.o  showbox.f
> g77 -O2 -fno-automatic -fno-second-underscore -o showbox  showbox.o
...
> cd grid && make install
> gcc -c  -O2 -o grid.o  grid.c
> gcc -c  -O2 -o score.o  score.c
> gcc -c  -O2 -o score_grid.o  score_grid.c
> g77 -c -O2 -fno-automatic -fno-second-underscore -o gridpoint.o  gridpoint.f
> gcc -c  -O2 -o define.o  define.c
> gcc -c  -O2 -o io.o  io.c
> gcc -c  -O2 -o io_grid.o  io_grid.c
> g77 -c -O2 -fno-automatic -fno-second-underscore -o io_gridf.o  io_gridf.f
> io_gridf.f: In function ‘readgrid’:
> io_gridf.f:69: warning: Function return value not set
> gcc -c  -O2 -o mol_prep.o  mol_prep.c
> gcc -c  -O2 -o io_receptor.o  io_receptor.c
> gcc -c  -O2 -o io_mol2.o  io_mol2.c
> gcc -c  -O2 -o io_pdb.o  io_pdb.c
> gcc -c  -O2 -o io_ptr.o  io_ptr.c
> gcc -c  -O2 -o io_sph.o  io_sph.c
> gcc -c  -O2 -o label.o  label.c
> gcc -c  -O2 -o label_node.o  label_node.c
> gcc -c  -O2 -o label_chem.o  label_chem.c
> gcc -c  -O2 -o label_vdw.o  label_vdw.c
> gcc -c  -O2 -o label_flex.o  label_flex.c
> gcc -c  -O2 -o mol.o  mol.c
> gcc -c  -O2 -o search.o  search.c
> gcc -c  -O2 -o transform.o  transform.c
> g77 -c -O2 -fno-automatic -fno-second-underscore -o transformf.o  transformf.f
> gcc -c  -O2 -o parm.o  parm.c
> parm.c: In function ‘set_memory_limit’:
> parm.c:404: warning: format ‘%d’ expects type ‘int’, but argument 4 has type ‘rlim_t’
> gcc -c  -O2 -o parm_grid.o  parm_grid.c
> gcc -c  -O2 -o rotrans.o  rotrans.c
> gcc -c  -O2 -o utility.o  utility.c
> gcc -c  -O2 -o vector.o  vector.c
> g77  -O2 -fno-automatic -fno-second-underscore grid.o score.o score_grid.o gridpoint.o define.o io.o io_grid.o io_gridf.o mol_prep.o io_receptor.o io_mol2.o io_pdb.o io_ptr.o io_sph.o label.o label_node.o label_chem.o label_vdw.o label_flex.o mol.o search.o transform.o transformf.o parm.o parm_grid.o rotrans.o utility.o vector.o -lm -lpthread -o grid \
>             
> ld: warning: in grid.o, file was built for unsupported file format which is not the architecture being linked (i386)
> ld: warning: in score.o, file was built for unsupported file format which is not the architecture being linked (i386)
> ld: warning: in score_grid.o, file was built for unsupported file format which is not the architecture being linked (i386)
> ld: warning: in define.o, file was built for unsupported file format which is not the architecture being linked (i386)
> ld: warning: in io.o, file was built for unsupported file format which is not the architecture being linked (i386)
> ld: warning: in io_grid.o, file was built for unsupported file format which is not the architecture being linked (i386)
> ld: warning: in mol_prep.o, file was built for unsupported file format which is not the architecture being linked (i386)
> ld: warning: in io_receptor.o, file was built for unsupported file format which is not the architecture being linked (i386)
> ld: warning: in io_mol2.o, file was built for unsupported file format which is not the architecture being linked (i386)
> ld: warning: in io_pdb.o, file was built for unsupported file format which is not the architecture being linked (i386)
> ld: warning: in io_ptr.o, file was built for unsupported file format which is not the architecture being linked (i386)
> ld: warning: in io_sph.o, file was built for unsupported file format which is not the architecture being linked (i386)
> ld: warning: in label.o, file was built for unsupported file format which is not the architecture being linked (i386)
> ld: warning: in label_node.o, file was built for unsupported file format which is not the architecture being linked (i386)
> ld: warning: in label_chem.o, file was built for unsupported file format which is not the architecture being linked (i386)
> ld: warning: in label_vdw.o, file was built for unsupported file format which is not the architecture being linked (i386)
> ld: warning: in label_flex.o, file was built for unsupported file format which is not the architecture being linked (i386)
> ld: warning: in mol.o, file was built for unsupported file format which is not the architecture being linked (i386)
> ld: warning: in search.o, file was built for unsupported file format which is not the architecture being linked (i386)
> ld: warning: in transform.o, file was built for unsupported file format which is not the architecture being linked (i386)
> ld: warning: in parm.o, file was built for unsupported file format which is not the architecture being linked (i386)
> ld: warning: in parm_grid.o, file was built for unsupported file format which is not the architecture being linked (i386)
> ld: warning: in rotrans.o, file was built for unsupported file format which is not the architecture being linked (i386)
> ld: warning: in utility.o, file was built for unsupported file format which is not the architecture being linked (i386)
> ld: warning: in vector.o, file was built for unsupported file format which is not the architecture being linked (i386)
> Undefined symbols:
>   "_MAIN__", referenced from:
>       _main in libgfortranbegin.a(fmain.o)
> ld: symbol(s) not found
> collect2: ld returned 1 exit status
> make[2]: *** [grid] Error 1
> make[1]: *** [utils] Error 2
> make: *** [install] Error 2
> ~~~~~~~~~~~~~~~~~~~~
> 
> I also googled the architecture warning and found the following link (http://www.qtcentre.org/threads/30670-On-Mac-quot-...file-was-built-for-unsupported-file-format..-quot-SOLVED).  Accordingly, I tried editing the /install/config.h file to: 'CC=          gcc -arch i386' and 'CXX=        g++ -arch i386'.  Running 'make all' after the edits above gave the following error:
> 
> ~~~~~~~~~~~~~~~~~~~~
> simbios-flores-2:install Jennifer$ make all
> Starting installation of 
> DOCK v6.4
> at Fri Apr 22 12:20:50 PDT 2011.
> 
> cd ../src && make install
> cd dock && make install
> ../../install/config.h:2: *** missing separator.  Stop.
> make[1]: *** [dock6] Error 2
> make: *** [install] Error 2
> ~~~~~~~~~~~~~~~~~~~~
> 
> 
> On Apr 21, 2011, at 11:22 PM, Scott Brozell wrote:
> > Goooggggggling on
> > _main in libgfortranbegin.a(fmain.o)
> > http://macresearch.org/undefined-symbols-gfortran
> > So check for ^M in the files you edited.
> > 
> > Another possibility is the gnu compiler(s) version(s).
> > If the above does not work then send verbose and verbatim details
> > on your compiler versions.
> > 
> > scott
> > 
> > On Wed, Apr 20, 2011 at 10:51:57AM -0700, Jennifer Lahti wrote:
> >> I am running into the following trouble trying to install DOCK 6.4 on Mac OSX Snow Leopard:
> >> 
> >> After configuring the Makefile using the gnu configuration file, I manually edited the install/config.h file so that the Fortran compiler is gfortran instead of g77.  I then attempted to build all DOCK programs and got the following error:
> >> /
> >> Undefined symbols:
> >>  "_MAIN__", referenced from:
> >>      _main in libgfortranbegin.a(fmain.o)
> >> ld: symbol(s) not found
> >> collect2: ld returned 1 exit status
> >> make[2]: *** [grid] Error 1


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