[Dock-fans] Fwd: Bug and new licence

Trent E. Balius tbalius at aol.com
Tue Dec 9 19:52:51 PST 2014



 

 

-----Original Message-----
From: Varun Venkatesh <varunjvenkatesh at gmail.com>
To: Trent E. Balius <tbalius at aol.com>
Cc: dock-fans <dock-fans at docking.org>
Sent: Tue, Dec 9, 2014 5:28 pm
Subject: Re: Bug and new licence


Dear Trent,


Here is the error. Could you post it for me?

In file included from score_chemgrid.cpp:38:
In file included from ./tnt/tnt.h:48:
./tnt/tnt_fortran_array1d.h:224:15: warning: '&&' within '||' [-Wlogical-op-parentheses]

        if ((i0 > 0) && (i1 < n_) || (i0 <= i1))
            ~~~~~~~~~^~~~~~~~~~~~ ~~
./tnt/tnt_fortran_array1d.h:224:15: note: place parentheses around the '&&' expression to silence this warning
        if ((i0 > 0) && (i1 < n_) || (i0 <= i1))
                     ^
            (                    )
In file included from score_chemgrid.cpp:38:
In file included from ./tnt/tnt.h:55:
./tnt/tnt_sparse_matrix_csr.h:97:3: error: no matching constructor for initialization of 'Array1D<int>'
                rowptr_(M, r), colind_(nz, c), dim1_(M), dim2_(N) {}
                ^       ~~~~
./tnt/tnt_array1d.h:63:11: note: candidate constructor not viable: no known conversion from 'const int *' to 'const int' for 2nd argument; dereference the argument with *
                 Array1D(int n, const T &a);
                 ^
./tnt/tnt_array1d.h:64:11: note: candidate constructor not viable: 2nd argument ('const int *') would lose const qualifier
                 Array1D(int n,  T *a);
                 ^
./tnt/tnt_array1d.h:61:11: note: candidate constructor not viable: requires 0 arguments, but 2 were provided
                 Array1D();
                 ^
./tnt/tnt_array1d.h:62:11: note: candidate constructor not viable: requires single argument 'n', but 2 arguments were provided
        explicit Array1D(int n);
                 ^
./tnt/tnt_array1d.h:65:14: note: candidate constructor not viable: requires single argument 'A', but 2 arguments were provided
    inline   Array1D(const Array1D &A);
             ^
In file included from score_chemgrid.cpp:38:
In file included from ./tnt/tnt.h:55:
./tnt/tnt_sparse_matrix_csr.h:97:18: error: no matching constructor for initialization of 'Array1D<int>'
                rowptr_(M, r), colind_(nz, c), dim1_(M), dim2_(N) {}
                               ^       ~~~~~
./tnt/tnt_array1d.h:63:11: note: candidate constructor not viable: no known conversion from 'const int *' to 'const int' for 2nd argument; dereference the argument with *
                 Array1D(int n, const T &a);
                 ^
./tnt/tnt_array1d.h:64:11: note: candidate constructor not viable: 2nd argument ('const int *') would lose const qualifier
                 Array1D(int n,  T *a);
                 ^
./tnt/tnt_array1d.h:61:11: note: candidate constructor not viable: requires 0 arguments, but 2 were provided
                 Array1D();
                 ^
./tnt/tnt_array1d.h:62:11: note: candidate constructor not viable: requires single argument 'n', but 2 arguments were provided
        explicit Array1D(int n);
                 ^
./tnt/tnt_array1d.h:65:14: note: candidate constructor not viable: requires single argument 'A', but 2 arguments were provided
    inline   Array1D(const Array1D &A);
             ^
2 warnings and 2 errors generated.
make[2]: *** [score_chemgrid.o] Error 1
make[1]: *** [dock6] Error 2
make: *** [install] Error 2



On Tue, Dec 9, 2014 at 8:28 AM, Trent E. Balius <tbalius at aol.com> wrote:

 Hi Varrun, 

I am not a mac user so maybe someone else can help. 

Please inclued your error message as text (the image is too big to post)
in the body of the email.

Also be sure to "make clean".  This is some time a source of errors. 

Take care

 

Trent

 

 

-----Original Message-----
From: Trent E. Balius <tbalius at aol.com>

To: dock-fans <dock-fans at docking.org>; varunjvenkatesh <varunjvenkatesh at gmail.com>
Sent: Tue, Dec 9, 2014 8:21 am
Subject: Fwd: Bug and new licence


 Hi Varun,

I am not a mac user so maybe someone else can help. 


 Unfortunately, we do not distribute older versions of the DOCK 5/6.  
This is because these version have bugs that have be fixed in the newer versions.

These older versions are unlikely to work either on your machine, if DOCK6.6 doesn't. 

Take care,

Trent


======================================
Trent E. Balius, PhD
Postdoc, Shoichet Lab, 
Dept. Pharm. Chem., UCSF
Phone: (415) 514-4253
URL: http://docking.org/~tbalius
======================================

 

 

-----Original Message-----
From: Varun Venkatesh <varunjvenkatesh at gmail.com>
To: Trent E. Balius <tbalius at aol.com>; dock-fans <dock-fans at docking.org>; dock_industry <dock_industry at dock.compbio.ucsf.edu>; dock_bugs <dock_bugs at dock.compbio.ucsf.edu>; dock_license <dock_license at dock.compbio.ucsf.edu>; jir322 <jir322 at gmail.com>
Sent: Mon, Dec 8, 2014 9:46 pm
Subject: Fwd: Bug and new licence



Dear John, Trent,




Here is a screenshot of my error. I am not able to post to dock-fans.  Can one of you do that?
I need this fixed urgently for my project.  If DOCK 6.6 has issues with mac, I would like to use an older version of DOCK.


Regards,
Varun




On Fri, Dec 5, 2014 at 7:52 PM, Trent E. Balius <tbalius at aol.com> wrote:

 Hi Varun,

I am sending this mail to the dock-fans list also.

Could you send us the exact error mesage which prints to you screen?
this is so that we can help you debug the problem. 

Take care,

Trent

 

======================================
Trent E. Balius, PhD
Postdoc, Shoichet Lab, 
Dept. Pharm. Chem., UCSF
Phone: (415) 514-4253
URL: http://docking.org/~tbalius
======================================


 

 

-----Original Message-----
From: Varun Venkatesh <varunjvenkatesh at gmail.com>
To: dock_bugs <dock_bugs at dock.compbio.ucsf.edu>; dock_license <dock_license at dock.compbio.ucsf.edu>; dock_industry <dock_industry at dock.compbio.ucsf.edu>
Sent: Fri, Dec 5, 2014 5:56 pm
Subject: Bug and new licence


Hi,


I just wanted to send this email because I experienced a bug in the DOCK 6.6 software. When I try to run and compile the program, it immediately creates 2 errors, which I found are embedded in the code of the program itself.  They were errors about a vector h missing and I am not able to debug this. Do you have a solution, or could I possibly get a licence earlier version of the program? 


Thank you,


Varun Venkatesh

















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