[Dock-fans] problem g77 using ubuntu 9.04 and headers missing for dock executables

Davide Mercadante dmer018 at aucklanduni.ac.nz
Thu May 28 01:50:23 PDT 2009


Dear Dock-fans mailing list,

I have tried to build the executables for DOCK6 and all its utilities after
the creation of the configuration file (./configure gnu) using the command:
make all.

Unfortunately I was not able to create the executables because the machine
gave me this error message:

*The DOCK configuration file has been created.
dmer018 at dmer018-laptop:~/Scrivania/dock6/install$ make all
Starting installation of
DOCK v6.2
at gio mag 28 12:24:55 NZST 2009.

cd ../src && make install
make[1]: ingresso nella directory «/home/dmer018/Scrivania/dock6/src»
cd dock && make install
make[2]: ingresso nella directory «/home/dmer018/Scrivania/dock6/src/dock»
g++ -c  -O2 -o amber_typer.o  amber_typer.cpp
amber_typer.cpp: In function ‘char* white_line(char*)’:
amber_typer.cpp:15: error: ‘strlen’ was not declared in this scope
amber_typer.cpp: In function ‘int assign_node(ATOM_TYPE_NODE&, int)’:
amber_typer.cpp:66: error: ‘strtok’ was not declared in this scope
amber_typer.cpp:66: error: ‘strcpy’ was not declared in this scope
amber_typer.cpp:87: error: ‘strncmp’ was not declared in this scope
amber_typer.cpp: In function ‘int check_type(const char*, const char*)’:
amber_typer.cpp:125: error: ‘strstr’ was not declared in this scope
amber_typer.cpp: In constructor ‘ATOM_TYPE::ATOM_TYPE()’:
amber_typer.cpp:251: error: ‘INT_MIN’ was not declared in this scope
amber_typer.cpp: In member function ‘void
ATOM_TYPER::get_vdw_labels(std::string, bool)’:
amber_typer.cpp:285: error: ‘strncmp’ was not declared in this scope
amber_typer.cpp:346: error: ‘strtok’ was not declared in this scope
amber_typer.cpp:382: error: ‘INT_MIN’ was not declared in this scope
amber_typer.cpp:387: error: ‘INT_MIN’ was not declared in this scope
amber_typer.cpp: In member function ‘int
ATOM_TYPER::assign_vdw_labels(DOCKMol&, int)’:
amber_typer.cpp:475: error: ‘strcmp’ was not declared in this scope
amber_typer.cpp: In member function ‘void
BOND_TYPER::get_flex_labels(std::string)’:
amber_typer.cpp:531: error: ‘strncmp’ was not declared in this scope
amber_typer.cpp:544: error: ‘strlen’ was not declared in this scope
amber_typer.cpp:561: error: ‘strtok’ was not declared in this scope
amber_typer.cpp: In member function ‘void
BOND_TYPER::get_flex_search(std::string)’:
amber_typer.cpp:598: error: ‘strtok’ was not declared in this scope
amber_typer.cpp:600: error: ‘strcmp’ was not declared in this scope
amber_typer.cpp: In member function ‘void
CHEM_TYPER::get_chem_labels(std::string)’:
amber_typer.cpp:753: error: ‘strncmp’ was not declared in this scope
amber_typer.cpp:762: error: ‘strtok’ was not declared in this scope
make[2]: *** [amber_typer.o] Errore 1
make[2]: uscita dalla directory «/home/dmer018/Scrivania/dock6/src/dock»
make[1]: *** [dock6] Errore 2
make[1]: uscita dalla directory «/home/dmer018/Scrivania/dock6/src»
make: *** [install] Errore 2

*I have solved this problem inserting some heading missing in some of the
files present in the folder ../dock6/src/dock/

I list here the headers missing that I found hoping that someone cant ake
advantage from the experience I had.
The files to correct are:

amber_typer.cpp ; conf_gen.cpp ; dockmol.cpp ; library_file.cpp ; orient.cpp
; score.cpp ; simplex.cpp ; sphere.cpp ; utils.cpp .*

The header that need to be added are the following:

amber_typer.cpp

#include <stdio.h>
#include <limits.h>

conf_gen.cpp

**#include <limits.h>

dockmol.cpp

#include <string.h>

orient.cpp

**#include <string.h>

score.cpp

#include <string.h>

simplex.cpp

#include <string.h>

sphere.cpp

#include <stdio.h>
#include <string.h>

utils.cpp

#include <string.h>

*Hope this can helps.*

However, continuing the building of the executables in the phase of creation
of the directories for the accessories I had the problem that the machine
was not able to find the command g77.
Obviously I tried to install the g77 compiler but with the ubuntu 9.04 (the
release on which I am installing dock) I was not able to install it for a
problem of unsolved dependencies that I was not able to solve.

There is the possibility to continue the installation using another
compiler?
Please, anyone knows how I can solve this problem?
Seems that g77 would be available only for the Hardy release of Ubuntu 7.10
(also for the version 8.10 is not available but have been substituted by
fort77).

Thanks infinitely in advance for any advice.

Cheers,
Davide

Davide Mercadante
PhD Student - Department of Chemistry -
Rm 438 ext. 89171
Faculty of Science
The University of Auckland
Auckland, New Zealand

*
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