[Dock-fans] errors with ubuntu 8.1 install

John J. Irwin jji at cgl.ucsf.edu
Thu Jan 22 09:58:42 PST 2009


Hi  -

It looks as if you didn't do make clean after ./configure gnu, which is
what ./configure asked you to do.   To see what make distclean means,
you can just look at the Makefile to see what it does. But you don't
need to really *understand* what make distclean does other than "it gets
rid of temporary files and machine specific files that could cause
problems during a full build of the software". Moreover, from the
transcript below, it seems you have not done make distclean.  If you are
reluctant to make distclean because you are worried it will wipe out the
hand editing you did, you can always tar a copy of the directory before
you do it.

Please let us know how it goes.

John
UCSF DOCK Team


William Stone wrote:
> I have attempted to install dock6.2 on two computer (under ubuntu 8.1
> distro) and get this same error messages as detailed by Imtiaz M
> (Firdy, 29 Aug 2008).  Scott Brozell (Wed Sept 33) suggested a number
> of fixes for these errors which I attempted to make by correcting the
> identified cpp files with the indicated #include headers, i.e., used
> gedit to modify all noted *.cpps and then started at "./configure gnu"
> followed by "make all # builds all the DOCK programs": the following
> is the terminal output.  I am uncertain as to what "make distclean"
> means and if this is the cause of the problems below.  Any help will
> be much appreciated- Thanks
>
> billstone at ubuntu:~$ ccd dock6/install
> bash: ccd: command not found
> billstone at ubuntu:~$ cd dock6/install
> billstone at ubuntu:~/dock6/install$ ./configure
>
> The configuration file exists with the creation stamp:
> # Created at Wed Jan 21 15:45:07 EST 2009 via ./configure gnu
>
> Usage: configure [-help] [compiler/platform [parallel] [pbsa] ]
>
> Installation Summary
>       configure is the first step in the installation procedure.
>       The second step is to build the desired DOCK executable(s)
>       with one of these make commands executed from this directory:
>       make all   # builds all the DOCK programs
>       make dock  # builds only the dock program
>       make utils # builds only the utilities programs
>       The final step is to test the desired DOCK executable(s)
>       with one of these make commands executed from the test subdirectory:
>       make all   # tests all the DOCK programs
>       make dock  # tests only the dock program
>       make utils # tests only the utilities programs
>
> Description
>       Create the DOCK configuration file, ../install/config.h,
>       by copying an existing configuration file that is selected using
>       the arguments.
>       When invoked without arguments, print this usage statement and
>       if the configuration file exists then print its creation stamp.
>       Some configuration files require that environment variables be
>       defined; these requirements are listed in the files and emitted
>       by configure.  Some configuration files contain
>       troubleshooting sections that describe corrective measures
>       for common difficulties.
>
> Options
>       -help
>               emit the usage statement.
>
> Notes
>       Configuration filename completion is not supported:
>       if there is only one config file for e.g., sunos, say,
>       sunos.parallel, then all arguments to configure are required:
>       configure sunos parallel
>
> Available configurations are
> gnu
> gnu parallel
> gnu parallel pbsa
> gnu pbsa
> sgi
> sgi parallel
> sgi parallel pbsa
> sgi pbsa
>
> billstone at ubuntu:~/dock6/install$ ./configure gnu
> The requested configuration file was found.
>
> Warning: the configuration file already exists with the creation stamp:
> # Created at Wed Jan 21 15:45:07 EST 2009 via ./configure gnu
> It will be overwritten !
> Don't forget to make clean before rebuilding.
> The best way to reconfigure and rebuild is to start with make distclean.
> Reconfiguring after make distclean will avoid this warning.
>
> The DOCK configuration file has been created.
> billstone at ubuntu:~/dock6/install$ make all # build all the DOCK programs
> Starting installation of
> DOCK v6.2
> at Thu Jan 22 10:01:25 EST 2009.
>
> cd ../src && make install
> make[1]: Entering directory `/home/billstone/dock6/src'
> cd dock && make install
> make[2]: Entering directory `/home/billstone/dock6/src/dock'
> g++ -c  -O2 -o amber_typer.o  amber_typer.cpp
> g++ -c  -O2 -o base_grid.o  base_grid.cpp
> base_grid.cpp: In member function 'void
> Base_Grid::read_header(std::string)':
> base_grid.cpp:33: warning: ignoring return value of 'size_t
> fread(void*, size_t, size_t, FILE*)', declared with attribute
> warn_unused_result
> base_grid.cpp:34: warning: ignoring return value of 'size_t
> fread(void*, size_t, size_t, FILE*)', declared with attribute
> warn_unused_result
> base_grid.cpp:35: warning: ignoring return value of 'size_t
> fread(void*, size_t, size_t, FILE*)', declared with attribute
> warn_unused_result
> base_grid.cpp:36: warning: ignoring return value of 'size_t
> fread(void*, size_t, size_t, FILE*)', declared with attribute
> warn_unused_result
> g++ -c  -O2 -o base_mpi.o  base_mpi.cpp
> g++ -c  -O2 -o base_score.o  base_score.cpp
> g++ -c  -O2 -o conf_gen.o  conf_gen.cpp
> g++ -c  -O2 -o dock.o  dock.cpp
> In file included from dock.cpp:10:
> version.h:6: warning: deprecated conversion from string constant to
> 'char*'
> version.h:8: warning: deprecated conversion from string constant to
> 'char*'
> dock.cpp: In function 'int main(int, char**)':
> dock.cpp:70: warning: deprecated conversion from string constant to
> 'char*'
> dock.cpp:74: warning: deprecated conversion from string constant to
> 'char*'
> dock.cpp:78: warning: deprecated conversion from string constant to
> 'char*'
> dock.cpp:82: warning: deprecated conversion from string constant to
> 'char*'
> dock.cpp:86: warning: ignoring return value of 'FILE* freopen(const
> char*, const char*, FILE*)', declared with attribute warn_unused_result
> g++ -c  -O2 -o dockmol.o  dockmol.cpp
> dockmol.cpp: In function 'bool Read_Mol2(DOCKMol&, std::istream&,
> bool, bool, bool)':
> dockmol.cpp:54: error: 'strncmp' was not declared in this scope
> dockmol.cpp:68: error: 'strncmp' was not declared in this scope
> dockmol.cpp:151: error: 'strncmp' was not declared in this scope
> dockmol.cpp:196: error: 'strncmp' was not declared in this scope
> dockmol.cpp:235: error: 'strncmp' was not declared in this scope
> dockmol.cpp:287: error: 'strncmp' was not declared in this scope
> dockmol.cpp: In member function 'std::vector<int, std::allocator<int>
> > DOCKMol::get_atom_children(int, int)':
> dockmol.cpp:942: error: 'memset' was not declared in this scope
> make[2]: *** [dockmol.o] Error 1
> make[2]: Leaving directory `/home/billstone/dock6/src/dock'
> make[1]: *** [dock6] Error 2
> make[1]: Leaving directory `/home/billstone/dock6/src'
> make: *** [install] Error 2
> billstone at ubuntu:~/dock6/install
>
> -- 
> Bill Stone, PhD
>
> ------------------------------------------------------------------------
>
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