[Dock-fans] errors with ubuntu 8.1 install

Scott Brozell sbrozell at scripps.edu
Thu Jan 22 14:38:09 PST 2009


Hi,

> > dockmol.cpp:54: error: 'strncmp' was not declared in this scope

add to the head of file dockmol.cpp
#include <string.h>

This one was missing from the list in
http://blur.compbio.ucsf.edu/pipermail/dock-fans/2008-September/001706.html

Scott

On Thu, 22 Jan 2009, John J. Irwin wrote:

> 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


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