[Dock-fans] errors with ubuntu 8.1 install

William Stone drbillstone at gmail.com
Thu Jan 22 07:34:25 PST 2009


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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