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

Michael Mysinger Michael.Mysinger at ucsf.edu
Thu May 28 14:34:57 PDT 2009


Hey Davide,

Thanks for posting the includes you needed to get it to compile with the 
newer g++. To answer you question regarding g77, the usual replacement 
is gfortran.  If changing FC to gfortran is not enough, try adding the 
'-ff2c' argument to get better backwards compatibility with g77.

Hope this helps,
Michael Mysinger
UCSF DOCK Team

Davide Mercadante wrote:
> 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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